filesystem Update Error /bin exists in filesystem

Alambre · 2013-06-01 07:15:23

it works, and is the very easy way, symlinks are automagicaly created on install filesystem. //off (if you install bash, su not works, yaourt too, sudo only works -> sudo bash )
Sorry for my mistake with code tags

Last edited by Alambre (2013-06-01 07:16:16)

Roken · 2013-06-01 07:37:04

For my part I hadn't realised I still had files in /bin and /sbin (all part of burg). Copied them to /usr/bin and then I had to manually delete /bin, /sbin and /usr/sbin before I could complete the upgrade. However, seems fine now.

combuster · 2013-06-01 08:14:24

Jodell wrote:

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

I'm positive. I can not remember if I exited root privileges and stayed on the same terminal as user or closed the terminal and tried to fire another from the same xfce session but it didn't work. Complained about /bin/bash. Couldn't login even when I tried to get to tty1 with ctrl+alt+f1, gave me to enter root as username but then nothing, stayed there and didnt asked me for a password. I knew then what I have done...

Only trouble I have is with dma, when I've tried to rebuild it, it complained about cheksum of the archive, even when I've changed it from the pkgbuild to match it propperly.

/edit: this is curls fault or something wrong from the download path (it reports downloading 125% of the archive)

/edit again: following the comment from the aur worked, I don't know how I've managed to calculate the cheksum wrong with the sha256sum

Last edited by combuster (2013-06-01 08:22:26)

progandy · 2013-06-01 10:27:00

Allan wrote:

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.

I found at least one of my problems. It is not directly post_install, but the shebang in e.g. locale-gen (glibc). Damn /bin/sh. Maybe something like this would work:

pacman -Sy bash glibc filesystem-update # filesystem-update contains essential symlinks like /bin/sh, /bin/bash, /bin/true, /bin/false, /sbin/ldconfig
pacman -Syu --ignore filesystem
pacman -S filesystem # filesystem `replaces` filesystem-update

Last edited by progandy (2013-06-01 10:29:24)

dbdii407 · 2013-06-01 12:28:02

So I'm a little confused as to the solution to this issue. What is it?

WonderWoofy · 2013-06-01 15:45:06

dbdii407 wrote:

So I'm a little confused as to the solution to this issue. What is it?

Did you read the thread?

sbfreak · 2013-06-01 16:41:29

Can I remove /bin, /sbin, and /usr/sbin after I've finished the update ?

Last edited by sbfreak (2013-06-01 16:41:46)

WorMzy · 2013-06-01 16:46:50

No, some files and binaries rely on hardcoded paths. (e.g. /etc/password probably lists your shell as /bin/bash, or /bin/zsh, or whatever). The symlinks pointing to /usr/bin allow these hardcoded paths to keep working.

Roken · 2013-06-01 16:59:19

WorMzy wrote:

No, some files and binaries rely on hardcoded paths. (e.g. /etc/password probably lists your shell as /bin/bash, or /bin/zsh, or whatever). The symlinks pointing to /usr/bin allow these hardcoded paths to keep working.

To add, for clarity, the filesystem update creates the links for you.

jim_bo · 2013-06-01 20:23:10

I have find an easy wait to update to filesystem 2013.03-1 atctually in testing.

Just remove the initscript package that is not supported due to systemd transition

 pacman -R initscript

karol · 2013-06-01 20:31:39

jim_bo wrote:

I have find an easy wait to update to filesystem 2013.03-1 atctually in testing.
Just remove the initscript package that is not supported due to systemd transition
 pacman -R initscript 

Currently 2013.05-2 is in testing and 2013.03-2 is in core so ...

Removing initscripts and installing systemd-sysvcompat is one of the steps of the initscripts -> systemd transition: https://wiki.archlinux.org/index.php/Sy … stallation

Last edited by karol (2013-06-01 20:32:13)

hcra · 2013-06-02 04:32:57

I followed the advice in the [testing] mailing list(noted in reply #3) and issued

comm -12 <(pacman -Qqm) <(pacman -Qqo /bin /sbin /usr/sbin | sort -u)

It returned no errors, so I (skipped Step 2) and proceeded with Step 3. pacman -Su. Disaster: filesystem failed to upgrade because of conflicting files.

A word to the wise: don't do this unless you know what you're doing. I broke my system, and, given that I'm a newbie, restored a recent image and downgraded from [testing].

jasonwryan · 2013-06-02 04:47:56

hcra wrote:

so I (skipped Step 2) and proceeded with Step 3. pacman -Su. Disaster: filesystem failed to upgrade because of conflicting files.

Step 3 is not pacman -Su.

3) Update your system:
$ pacman -Syu --ignore filesystem
$ pacman -Su

hcra · 2013-06-02 04:55:39

I'm very sorry for the confusion. I ran both commands in step 3; the first successfully. However I skipped: "Make sure any packages in IgnorePkg or IgnoreGroup do not have files in /bin, /sbin, or /usr/sbin. Fix them if necessary."

I'm not even sure how to do this.

karol · 2013-06-02 10:03:23

hcra wrote:

I'm very sorry for the confusion. I ran both commands in step 3; the first successfully. However I skipped: "Make sure any packages in IgnorePkg or IgnoreGroup do not have files in /bin, /sbin, or /usr/sbin. Fix them if necessary."
I'm not even sure how to do this.

grep the output 'pacman -Ql foo', where 'foo' is the ignored package.

soupcan · 2013-06-02 19:00:05

I'm having a similar problem to hcra. I ran

comm -12 <(pacman -Qqm) <(pacman -Qqo /bin /sbin /usr/sbin | sort -u)

Returned nothing, so I proceeded to do

pacman -Syu --ignore filesystem

Then ran

pacman -Su

This fails with /bin and /usr/sbin exists in filesystem. The first command never returned anything, just sat at a blank line until I Ctrl-C. Seems I still have packages with files there but I'm unsure of how to see which ones they are or what to do about them.

EDIT: just tried running the first command again, its actually listing packages now. Not sure why it wasn't completing the first time... I'm removing the packages and seeing if I can install filesystem after that.
EDIT2: Success. Still not sure why the comm command never returned anything the first time around, but I've got filesystem installed now and I'm on to fixing the offending packages.

Last edited by soupcan (2013-06-02 19:15:43)

shulamy · 2013-06-02 19:08:39

i updated my sestem few days ago and there was a

filesystem update to -2013.05-2.

there was an error of conflicting files

/bin /sbin and /usr/sbin exists in filesystem.

i ignored filesystem and i found myself without /bin and without /sbin

and at next boot the system booted to

error: rootdevice mounted successfully but /sbin/init does not exist.

sh: can't ecces tty: job control turned off.

[rootfs/]#

now i arch-chrooted from an installation disk after copying /bin and /sbin from it

(maybe a big mistake)

and update again by pacman -Syu

and i got the conflict again.

so my question is: is it safe to force the update

or shoud i look for another way to deal with it?

i read the posts on /sbin/init but in my case it was realy missing.

( i mounted the partition from fedora)

ezik

WorMzy · 2013-06-02 19:10:07

For "Ignored" packages where modifying the PKGBUILD and recompiling is either impossible or time consuming, you could move the files and update pacman's database manually (easy and quick enough, but you need to know what you're doing), or you could rebuild the package archive, fixing the directory structure, then install the new package archive with pacman -U. I've written a script for this purpose, if anybody is interested: https://github.com/WorMzy/converttousrbin

soupcan wrote:

Then ran
pacman -Su
. This fails with /bin and /usr/sbin exists in filesystem. The first command never returned anything, just sat at a blank line until I Ctrl-C.

How long did you wait?

karol · 2013-06-02 19:10:33

soupcan wrote:

Seems I still have packages with files there but I'm unsure of how to see which ones they are or what to do about them.

$ ls /bin

could help. Next,

$ pacman -Qo /bin/foo

WorMzy · 2013-06-02 19:12:02

See the stickied topic in [testing]. https://bbs.archlinux.org/viewtopic.php?id=164312

Last edited by WorMzy (2013-06-02 19:12:59)

karol · 2013-06-02 19:13:18

Are you subscribed to arch-dev-public ML?

Last edited by karol (2013-06-02 19:14:10)

soupcan · 2013-06-02 19:18:49

WorMzy wrote:

For "Ignored" packages where modifying the PKGBUILD and recompiling is either impossible or time consuming, you could move the files and update pacman's database manually (easy and quick enough, but you need to know what you're doing), or you could rebuild the package archive, fixing the directory structure, then install the new package archive with pacman -U. I've written a script for this purpose, if anybody is interested: https://github.com/WorMzy/converttousrbin
soupcan wrote:
Then ran
pacman -Su
. This fails with /bin and /usr/sbin exists in filesystem. The first command never returned anything, just sat at a blank line until I Ctrl-C.
How long did you wait?

Waited more than 10 minutes. When I ran it again, I just paged through my history and ran the same command, which completed instantly that time. I don't understand how that could be, but it's all set now.

@karol Couldn't use ls, since it was located in /bin

karol · 2013-06-02 19:23:27

soupcan wrote:

@karol Couldn't use ls, since it was located in /bin

You can always use a liveCD/ liveUSB :-)

Glad you found a way to un-break my heart your system ;P

jasonwryan · 2013-06-02 20:43:29

Merging with the stickied thread...

donniezazen · 2013-06-03 04:02:41

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

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

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

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?

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

Thanks.

Arch Linux

#26 2013-06-01 07:15:23

Re: filesystem Update Error /bin exists in filesystem

#27 2013-06-01 07:37:04

Re: filesystem Update Error /bin exists in filesystem

#28 2013-06-01 08:14:24

Re: filesystem Update Error /bin exists in filesystem

#29 2013-06-01 10:27:00

Re: filesystem Update Error /bin exists in filesystem

#30 2013-06-01 12:28:02

Re: filesystem Update Error /bin exists in filesystem

#31 2013-06-01 15:45:06

Re: filesystem Update Error /bin exists in filesystem

#32 2013-06-01 16:41:29

Re: filesystem Update Error /bin exists in filesystem

#33 2013-06-01 16:46:50

Re: filesystem Update Error /bin exists in filesystem

#34 2013-06-01 16:59:19

Re: filesystem Update Error /bin exists in filesystem

#35 2013-06-01 20:23:10

Re: filesystem Update Error /bin exists in filesystem

#36 2013-06-01 20:31:39

Re: filesystem Update Error /bin exists in filesystem

#37 2013-06-02 04:32:57

Re: filesystem Update Error /bin exists in filesystem

#38 2013-06-02 04:47:56

Re: filesystem Update Error /bin exists in filesystem

#39 2013-06-02 04:55:39

Re: filesystem Update Error /bin exists in filesystem

#40 2013-06-02 10:03:23

Re: filesystem Update Error /bin exists in filesystem

#41 2013-06-02 19:00:05

Re: filesystem Update Error /bin exists in filesystem

#42 2013-06-02 19:08:39

Re: filesystem Update Error /bin exists in filesystem

#43 2013-06-02 19:10:07

Re: filesystem Update Error /bin exists in filesystem

#44 2013-06-02 19:10:33

Re: filesystem Update Error /bin exists in filesystem

#45 2013-06-02 19:12:02

Re: filesystem Update Error /bin exists in filesystem

#46 2013-06-02 19:13:18

Re: filesystem Update Error /bin exists in filesystem

#47 2013-06-02 19:18:49

Re: filesystem Update Error /bin exists in filesystem

#48 2013-06-02 19:23:27

Re: filesystem Update Error /bin exists in filesystem

#49 2013-06-02 20:43:29

Re: filesystem Update Error /bin exists in filesystem

#50 2013-06-03 04:02:41

Re: filesystem Update Error /bin exists in filesystem

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