filesystem Update Error /bin exists in filesystem

Trilby · 2013-06-15 15:21:15

zero-giulio wrote:

I ran pacman -Syy... Then I try to do a pacman -S pacman.

Why on earth would you do that? That would break a system regardless of the filesystem update. Follow the instructions that have been provided on the front page news and in this thread over and over and over again

FIX: restore the backup (again), then follow the instructions properly.

Last edited by Trilby (2013-06-15 15:21:56)

Sandro · 2013-06-15 15:43:26

Don Coyote wrote:

I'm not sure if my sense of written language is in conflict with any others', but if the announcement:
5) Update your system.
Before performing this update, you may want to ensure you have a second terminal open with root privileges in the unlikely event of an emergency, particularly if updating over ssh.
# pacman -Syu --ignore filesystem,bash
# pacman -S bash
# pacman -Su
Had instead read:
5) Update your system.
(Before performing this update, you may want to ensure you have a second terminal open with root privileges in the unlikely event of an emergency, particularly if updating over ssh.)
# pacman -Syu --ignore filesystem,bash
# pacman -S bash
# pacman -Su
or
5) Before performing this update, you may want to ensure you have a second terminal open with root privileges in the unlikely event of an emergency, particularly if updating over ssh.
Update your system.
# pacman -Syu --ignore filesystem,bash
# pacman -S bash
# pacman -Su
It would have saved me a few hours of poking around the forums. The current formatting implies to me that the code block is a continuation of the supplementary instructions and the core instructions are simply to 'update your system', which continues to give the error. Yes, reading the 'suggestion' and contents of the block makes it clear the two are not conncected, but disregarding unneeded text is second nature when perusing the web, particularly branching instructions associated with an open system like this.

At first I thought the same thing about the code block at the end, it seems I wasn't the only one!

Scimmia · 2013-06-15 16:13:24

HeartsAlive wrote:

I still haven't solved this... tried reinstalling from outside the partition but I still get the failed to initialize alpm library problem. Do I need to mount something before pacman will work correctly from outside the partition?

Scimmia wrote:

HeartsAlive, that usually means you didn't mount all of the filesystems you need or you gave the wrong root.

swanson · 2013-06-15 16:17:50

Could still be like ximiric says. Look here:
https://bbs.archlinux.org/viewtopic.php?id=164631

HeartsAlive · 2013-06-15 16:48:38

Scimmia wrote:

HeartsAlive wrote:
I still haven't solved this... tried reinstalling from outside the partition but I still get the failed to initialize alpm library problem. Do I need to mount something before pacman will work correctly from outside the partition?
Scimmia wrote:
HeartsAlive, that usually means you didn't mount all of the filesystems you need or you gave the wrong root.

Telling me I didn't mount all the filesystems doesn't help me when I don't know what ones I should be mounting. I tried googling what ones I needed for pacman to work but the results are not helpful at all.

I tried the /etc/passwd and /etc/shells thing too but mine matched. I'm not getting a failure message at all when I try to login, it just prompts me to log in again.

shulamy · 2013-06-15 18:53:31

https://wiki.archlinux.org/index.php/Chroot

ezik

HeartsAlive · 2013-06-15 18:57:53

These are the instructions I originally followed but when I try to chroot I get chroot: failed to run command /bin/sh: Exec format error. Everywhere I looked told me I was getting this error because the architecture I was using on the liveusb was different than the architecture of my arch partition but they are both 64. I tried both options on the liveusb anyways but I got the same error.

WonderWoofy · 2013-06-15 18:58:34

HeartsAlive wrote:

Telling me I didn't mount all the filesystems doesn't help me when I don't know what ones I should be mounting. I tried googling what ones I needed for pacman to work but the results are not helpful at all.

Well, holding your hand and giving you a step by step about how to do this is not going to increase your google skills either. Nor will it help with your ability to search the wiki, which was pointed out in the post above.

jasonwryan · 2013-06-15 19:38:10

Merging with the sticky...

cfr · 2013-06-15 21:25:08

HeartsAlive wrote:

Scimmia wrote:
HeartsAlive, that usually means you didn't mount all of the filesystems you need or you gave the wrong root.
Telling me I didn't mount all the filesystems doesn't help me when I don't know what ones I should be mounting. I tried googling what ones I needed for pacman to work but the results are not helpful at all.

Why, if you are not sure, don't you mount them all in the appropriate places to be on the safe side? Sure, this might mean typing an extra couple of commands but that is surely a lot less work than googling, posting here and watching paint dry until you can fix your system. Is there some reason you are reluctant to do this?

HeartsAlive · 2013-06-15 21:37:30

I guess I don't know what you mean by mounting them all in the appropriate places. I just mount /dev/sda4 to /mnt. The chroot guide on the wiki has the instructions to mount temporary file systems and I thought that there where more temporary filesystems I had to mount to get pacman to work correctly and I couldn't find anywhere what those extra filesystems could be. I guess I should have been more clear in my first post but when I said I could not chroot, I had tried following the wiki step for step before posting that I was getting an error trying to chroot.

cfr · 2013-06-15 21:42:40

HeartsAlive wrote:

I guess I don't know what you mean by mounting them all in the appropriate places. I just mount /dev/sda4 to /mnt. The chroot guide on the wiki has the instructions to mount temporary file systems and I thought that there where more temporary filesystems I had to mount to get pacman to work correctly and I couldn't find anywhere what those extra filesystems could be. I guess I should have been more clear in my first post but when I said I could not chroot, I had tried following the wiki step for step before posting that I was getting an error trying to chroot.

Is that correct for your system? That is, you have a single partition for Arch on /dev/sda4? No separate /boot or /var or anything else?

What are the contents of /mnt/etc/fstab?

copacetic · 2013-06-16 07:42:30

Hello all,

It seems I've made a terrible mistake and now my arch is unbootable.

I attempted to do the filesystem update with the following commands (I'd found that thinkfan was one of the packages that needed removal):

# pacman -Syu --ignore filesystem
# pacman -Su
# pacman -R thinkfan
# pacman -Su
# pacman -S thinkfan
# yaourt -Syu
# shutdown -r now

The upgrade succeeded with no errors, but upon reboot, it says device not found and gives me a rootfs shell. I tried to follow Scimmia's recovery guide and made/booted from an arch install image.

Some investigation led me to find that /bin, /sbin, and /usr/sbin were all owned by the filesystem package. Also, /bin and /sbin are symlinks to /usr/bin, but /usr/sbin is not a symlink and is non-empty. I would really appreciate some help and will be actively trying to get my arch boot back... thank you.

Lone_Wolf · 2013-06-16 09:31:39

zero-giulio, when you do a pacman -S pacman , only pacman itself is updated and not it's dependencies.
(you found out the hard way why doing partial upgrades is a bad idea) .

you can try booting from a live cd/usb and then chrooot foolowed by pacman -Syu .

If you want to upgrade to pacakges from a specific date, always combine the use arm.konnichi trick with pacman -Syu .

Don Coyote wrote:

Yes, reading the 'suggestion' and contents of the block makes it clear the two are not conncected, but disregarding unneeded text is second nature when perusing the web, particularly branching instructions associated with an open system like this.

I agree that if you treat the news item like that, you can easily overlook the warning/suggestion.
Keep in mind that arch news items are intended to ONLY convey the necessary information, so all text matters.

stokker · 2013-06-16 10:43:50

I've used Archlinux since 2004, and this "move binaries into a unified /usr/bin directory." must be the worst/most unnecessary/stupid update to date.
I'm seriously thinking of changing to another distro, but I probably wont, because i like Arch. But this update really pissed me off!
One of the motivations for this change was "the old way is less K.I.S.S" - that's just BS.

I have 5 systems in my house running arch, It was not simple to work fix this (stupid) update...

/me disappointed

WorMzy · 2013-06-16 11:51:25

It is simple if you follow the instructions. The only things that can cause problems are unsupported packages, files you have manually created, and your own failure to follow the instructions on how to deal with these correctly/complete the update.

If you have have managed to break one or more of your systems,, read through this topic and find a solution.

solusipse · 2013-06-16 14:41:55

I had somewhat old installation of arch so I decided to reinstall it completly on my server to avoid that unfamous filesystem error. After reinstallation I simply typed 'pacman -Syu' and guess what

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.

It's probably provider's fault (old and messy installation image) but I was so amused by that situation that i couldn't resist to post that here. And it wasn't really hard to fix that at least.

Last edited by solusipse (2013-06-16 15:09:40)

Scimmia · 2013-06-16 15:11:57

copacetic wrote:

Hello all,
It seems I've made a terrible mistake and now my arch is unbootable.
I attempted to do the filesystem update with the following commands (I'd found that thinkfan was one of the packages that needed removal):
# pacman -Syu --ignore filesystem
# pacman -Su
# pacman -R thinkfan
# pacman -Su
# pacman -S thinkfan
# yaourt -Syu
# shutdown -r now
The upgrade succeeded with no errors, but upon reboot, it says device not found and gives me a rootfs shell. I tried to follow Scimmia's recovery guide and made/booted from an arch install image.
Some investigation led me to find that /bin, /sbin, and /usr/sbin were all owned by the filesystem package. Also, /bin and /sbin are symlinks to /usr/bin, but /usr/sbin is not a symlink and is non-empty. I would really appreciate some help and will be actively trying to get my arch boot back... thank you.

You forgot to ignore bash. Because of that, when the kernel upgrade tried to run mkinitcpio, it failed and was unable to generate a valid initramfs. You need to chroot into the system and regenerate it. The guide you mentioned is for people who didn't finish and the new filesystem package wasn't installed.

Don Coyote · 2013-06-16 16:26:46

Lone_Wolf wrote:

I agree that if you treat the news item like that, you can easily overlook the warning/suggestion.
Keep in mind that arch news items are intended to ONLY convey the necessary information, so all text matters.

The problem isn't that the warning is overlooked, but that the crucial information in the code block can easily be interpreted as part of the optional suggestion.

Pretty much everything on this site is necessary information, just not necessary to every individual. So it is with this announcement. The phrase "you may want to" implies something not needed to complete the task. As i had a very basic system with only official packages, i figured (correctly) that i didn't need the extra precaution so did not waste time trying to analyze it further, but as i said the formatting is less clear than it could be on which instructions the code block is attached to.

I'm not giving angry venting like so many disrespectful and ungrateful newbies are in this thread, just voicing my opinion that clear and logical instructions are essentially an extention of well commented and formatted code. If an important news item can be stated more clearly, it will probably help limit forum blowback from frustrated users.

cliffordsr · 2013-06-16 21:25:17

This is what happens when I attempt an -Syu

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace lib32-dbus-core with multilib/lib32-dbus? [Y/n] 
:: Replace turbojpeg with extra/libjpeg-turbo? [Y/n] 
resolving dependencies...
warning: dependency cycle detected:
warning: lib32-gcc-libs will be installed before its gcc-libs-multilib dependency
looking for inter-conflicts...

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                sed-4.2.2-3  shadow-4.1.5.1-6  shared-desktop-ontologies-0.11.0-1  skype-4.2.0.11-1  smbclient-4.0.6-1  soprano-2.9.2-1  sqlite-3.7.17-1  strigi-0.7.8-3  sudo-1.8.7-1  supertux-0.3.3-8  systemd-204-3  systemd-sysvcompat-204-3
                sysvinit-tools-2.88-11  tar-1.26-4  tcsh-6.18.01-2  transmission-qt-2.77-3  turbojpeg-1.2.1-1 [removal]  ucommon-6.0.5-1  udisks2-2.1.0-3  upower-0.9.20-2  usbmuxd-1.0.8-2  usbutils-007-1  util-linux-2.23.1-2  v4l-utils-0.9.5-2
                virtualbox-4.2.12-3  virtualbox-host-modules-4.2.12-8  virtualgl-2.3.2-4  virtuoso-base-6.1.6-2  vlc-2.0.7-2  vte-common-0.34.6-1  webkitgtk2-1.10.2-7  wireless_tools-29-8  wireshark-cli-1.10.0-2  wireshark-gtk-1.10.0-2  wpa_actiond-1.4-2
                wpa_supplicant-2.0-4  wxgtk-2.8.12.1-5  xerces-c-3.1.1-4  xf86-input-synaptics-1.7.1-1  xf86-video-intel-2.21.9-1  xfsprogs-3.1.11-1  xkeyboard-config-2.9-1  xorg-fonts-alias-1.0.3-1  xorg-xrefresh-1.0.5-1  xterm-293-1  zsh-5.0.2-2  zvbi-0.2.33-6

Total Installed Size:   -690.03 MiB
Net Upgrade Size:       -76.07 MiB

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

I have no idea what to do; I can't exactly get rid of /bin or /sbin or /usr/sbin.
Any ideas?
Thanks,
-Cliff

karol · 2013-06-16 21:28:28

Have you read the front page?

jasonwryan · 2013-06-16 21:29:39

karol wrote:

Have you read the front page?

Clearly not. Merging with the sticky...

copacetic · 2013-06-16 23:30:01

Scimmia wrote:

copacetic wrote:
Hello all,
It seems I've made a terrible mistake and now my arch is unbootable.
I attempted to do the filesystem update with the following commands (I'd found that thinkfan was one of the packages that needed removal):
# pacman -Syu --ignore filesystem
# pacman -Su
# pacman -R thinkfan
# pacman -Su
# pacman -S thinkfan
# yaourt -Syu
# shutdown -r now
The upgrade succeeded with no errors, but upon reboot, it says device not found and gives me a rootfs shell. I tried to follow Scimmia's recovery guide and made/booted from an arch install image.
Some investigation led me to find that /bin, /sbin, and /usr/sbin were all owned by the filesystem package. Also, /bin and /sbin are symlinks to /usr/bin, but /usr/sbin is not a symlink and is non-empty. I would really appreciate some help and will be actively trying to get my arch boot back... thank you.
You forgot to ignore bash. Because of that, when the kernel upgrade tried to run mkinitcpio, it failed and was unable to generate a valid initramfs. You need to chroot into the system and regenerate it. The guide you mentioned is for people who didn't finish and the new filesystem package wasn't installed.

Scimmia, I don't want to mess it up further so would you mind commenting on what I plan to do:
1. Chroot into my arch installation
2. mkinitcpio -p linux (I have a stock arch install)
3. reboot
4. Reinstall bash?

All help appreciated, thank you for your first reply.

cfr · 2013-06-16 23:46:31

@copacetic,
I think you will need to reinstall bash before you chroot to regenerate the image. Otherwise, you will be in just the same position as before and the generation will not succeed. You can use pacstrap or pacman (specifying the root etc.) to do this.

copacetic · 2013-06-17 00:37:58

Hey cfr and Scimmia,

I tried some stuff and thought I'd post my outputs:

When I attempted to do:

pacman --root -R bash -> error: failed to initialize alpm library (could not find or read directory)
After Chrooting:
pacman -S bash -> does not work because I guess I didn't mount proc or something along those lines..
mkinitcpio -p linux -> says proc must be mounted

I only have one mountpoint so I've been mounting with:

mount /mnt /dev/sda3 (sda3 is my linux install, this succeeds)

I then chrooted with:

chroot /mnt /usr/bin/bash (this also works)

All advice appreciated.. my next steps are going to be to figure out how to get proc mounted in the chroot, I guess.

Arch Linux

#601 2013-06-15 15:21:15

Re: filesystem Update Error /bin exists in filesystem

#602 2013-06-15 15:43:26

Re: filesystem Update Error /bin exists in filesystem

#603 2013-06-15 16:13:24

Re: filesystem Update Error /bin exists in filesystem

#604 2013-06-15 16:17:50

Re: filesystem Update Error /bin exists in filesystem

#605 2013-06-15 16:48:38

Re: filesystem Update Error /bin exists in filesystem

#606 2013-06-15 18:53:31

Re: filesystem Update Error /bin exists in filesystem

#607 2013-06-15 18:57:53

Re: filesystem Update Error /bin exists in filesystem

#608 2013-06-15 18:58:34

Re: filesystem Update Error /bin exists in filesystem

#609 2013-06-15 19:38:10

Re: filesystem Update Error /bin exists in filesystem

#610 2013-06-15 21:25:08

Re: filesystem Update Error /bin exists in filesystem

#611 2013-06-15 21:37:30

Re: filesystem Update Error /bin exists in filesystem

#612 2013-06-15 21:42:40

Re: filesystem Update Error /bin exists in filesystem

#613 2013-06-16 07:42:30

Re: filesystem Update Error /bin exists in filesystem

#614 2013-06-16 09:31:39

Re: filesystem Update Error /bin exists in filesystem

#615 2013-06-16 10:43:50

Re: filesystem Update Error /bin exists in filesystem

#616 2013-06-16 11:51:25

Re: filesystem Update Error /bin exists in filesystem

#617 2013-06-16 14:41:55

Re: filesystem Update Error /bin exists in filesystem

#618 2013-06-16 15:11:57

Re: filesystem Update Error /bin exists in filesystem

#619 2013-06-16 16:26:46

Re: filesystem Update Error /bin exists in filesystem

#620 2013-06-16 21:25:17

Re: filesystem Update Error /bin exists in filesystem

#621 2013-06-16 21:28:28

Re: filesystem Update Error /bin exists in filesystem

#622 2013-06-16 21:29:39

Re: filesystem Update Error /bin exists in filesystem

#623 2013-06-16 23:30:01

Re: filesystem Update Error /bin exists in filesystem

#624 2013-06-16 23:46:31

Re: filesystem Update Error /bin exists in filesystem

#625 2013-06-17 00:37:58

Re: filesystem Update Error /bin exists in filesystem

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