Arch Linux

tmuntan1

Member

Registered: 2014-11-14

Posts: 6

Update Problems with filesystem

Any time I try to update filesystem, I get "exists in filesystem" errors and it wont install.

I have found an issue similar to mine at https://www.archlinux.org/news/binaries … ervention/, but I don't really think that it is the same issue as it was from 2013 and I have more directories than just bin that have issues.

Here is the output from the "pacman -Syu" command.

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 archlinuxfr is up to date
 infinality-bundle is up to date
 infinality-bundle-multilib is up to date
 infinality-bundle-fonts is up to date
 atlassian is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Packages (1): filesystem-2014.10-3

Total Installed Size:   0.01 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: /etc/arch-release exists in filesystem
filesystem: /etc/mtab exists in filesystem
filesystem: /etc/profile.d/locale.sh exists in filesystem
filesystem: /lib exists in filesystem
filesystem: /lib64 exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/lib/modprobe.d/usb-load-ehci-first.conf exists in filesystem
filesystem: /usr/lib/os-release exists in filesystem
filesystem: /usr/lib64 exists in filesystem
filesystem: /usr/local/share/man exists in filesystem
filesystem: /usr/sbin exists in filesystem
filesystem: /usr/share/man/man7/archlinux.7.gz exists in filesystem
filesystem: /var/lock exists in filesystem
filesystem: /var/mail exists in filesystem
filesystem: /var/run exists in filesystem
Errors occurred, no packages were upgraded.

Does anyone have any advice?

Thank you for your help

arojas

Developer

From: Spain

Registered: 2011-10-09

Posts: 2,290

Re: Update Problems with filesystem

Looks like a borked database. What is your current filesystem version?

tmuntan1

Member

Registered: 2014-11-14

Posts: 6

Re: Update Problems with filesystem

It is currently at 2014.07-1

ewaller

Administrator

From: Pasadena, CA

Registered: 2009-07-13

Posts: 20,642

Re: Update Problems with filesystem

I have a feeling the problem stems from the archlinuxfr repository.  There were some recent threads about them and problems with how they package things, but I cannot find them right now.   My suggestion would be to remove the repository and try without it.  You might try it as a experiment at least.

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tmuntan1

Member

Registered: 2014-11-14

Posts: 6

Re: Update Problems with filesystem

I removed the repository, but the newly downloaded package didn't seem to help.  How bad would it be just to force the install?

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 infinality-bundle is up to date
 infinality-bundle-multilib is up to date
 infinality-bundle-fonts is up to date
 atlassian is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Packages (4): calibre-2.10.0-1  chromium-38.0.2125.122-1  filesystem-2014.10-3  nodejs-0.10.33-5

Total Download Size:    66.53 MiB
Total Installed Size:   249.39 MiB
Net Upgrade Size:       0.15 MiB

:: Proceed with installation? [Y/n] y
:: Retrieving packages ...
 filesystem-2014.10-3-x86_64                                                                            8.7 KiB  0.00B/s 00:00 [#############################################################################] 100%
 chromium-38.0.2125.122-1-x86_64                                                                       37.3 MiB   755K/s 00:51 [#############################################################################] 100%
 calibre-2.10.0-1-x86_64                                                                               24.8 MiB   884K/s 00:29 [#############################################################################] 100%
 nodejs-0.10.33-5-x86_64                                                                                4.4 MiB   880K/s 00:05 [#############################################################################] 100%
(4/4) checking keys in keyring                                                                                                 [#############################################################################] 100%
(4/4) checking package integrity                                                                                               [#############################################################################] 100%
(4/4) loading package files                                                                                                    [#############################################################################] 100%
(4/4) checking for file conflicts                                                                                              [#############################################################################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /bin exists in filesystem
filesystem: /etc/arch-release exists in filesystem
filesystem: /etc/mtab exists in filesystem
filesystem: /etc/profile.d/locale.sh exists in filesystem
filesystem: /lib exists in filesystem
filesystem: /lib64 exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/lib/modprobe.d/usb-load-ehci-first.conf exists in filesystem
filesystem: /usr/lib/os-release exists in filesystem
filesystem: /usr/lib64 exists in filesystem
filesystem: /usr/local/share/man exists in filesystem
filesystem: /usr/sbin exists in filesystem
filesystem: /usr/share/man/man7/archlinux.7.gz exists in filesystem
filesystem: /var/lock exists in filesystem
filesystem: /var/mail exists in filesystem
filesystem: /var/run exists in filesystem
Errors occurred, no packages were upgraded.

Trilby

Inspector Parrot

Registered: 2011-11-29

Posts: 30,459

Website

Re: Update Problems with filesystem

That wasn't newly downloaded - pacman is still just trying to use the one previously downloaded.  With that repository still removed (I'd remove / comment all but the basic ones for now) run `pacman -Scc` (respond yes), then try `pacman -Syu` again.

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"UNIX is simple and coherent" - Dennis Ritchie; "GNU's Not Unix" - Richard Stallman

WorMzy

Administrator

From: Scotland

Registered: 2010-06-16

Posts: 13,548

Website

Re: Update Problems with filesystem

I'd agree with arojas here. Can you post the output of:

cat /var/lib/pacman/local/filesystem-*/files

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tmuntan1

Member

Registered: 2014-11-14

Posts: 6

Re: Update Problems with filesystem

I removed it from /var/cache/pacman/pkg before I ran the install before, but I just ran the commands that recommended and it still didn't seem to help.

pkg » sudo pacman -Scc                                                                                                                                                                              Fri 14  5:45PM

Cache directory: /var/cache/pacman/pkg/
:: Do you want to remove ALL files from cache? [y/N] y
removing all files from cache...

Database directory: /var/lib/pacman/
:: Do you want to remove unused repositories? [Y/n] y
removing unused sync repositories...

pkg » sudo pacman -Syu                                                                                                                                                                              Fri 14  5:45PM
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 infinality-bundle is up to date
 infinality-bundle-multilib is up to date
 infinality-bundle-fonts is up to date
 atlassian is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Packages (1): filesystem-2014.10-3

Total Download Size:    0.01 MiB
Total Installed Size:   0.01 MiB

:: Proceed with installation? [Y/n] y
:: Retrieving packages ...
 filesystem-2014.10-3-x86_64                                                                            8.7 KiB  0.00B/s 00:00 [#############################################################################] 100%
(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: /etc/arch-release exists in filesystem
filesystem: /etc/mtab exists in filesystem
filesystem: /etc/profile.d/locale.sh exists in filesystem
filesystem: /lib exists in filesystem
filesystem: /lib64 exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/lib/modprobe.d/usb-load-ehci-first.conf exists in filesystem
filesystem: /usr/lib/os-release exists in filesystem
filesystem: /usr/lib64 exists in filesystem
filesystem: /usr/local/share/man exists in filesystem
filesystem: /usr/sbin exists in filesystem
filesystem: /usr/share/man/man7/archlinux.7.gz exists in filesystem
filesystem: /var/lock exists in filesystem
filesystem: /var/mail exists in filesystem
filesystem: /var/run exists in filesystem
Errors occurred, no packages were upgraded.

Thank you all for your help.

tmuntan1

Member

Registered: 2014-11-14

Posts: 6

Re: Update Problems with filesystem

I ran "cat /var/lib/pacman/local/filesystem-*/files" and "cat /var/lib/pacman/local/filesystem-2014.07-1/files", but it seems to be empty.

Last edited by tmuntan1 (2014-11-14 16:51:28)

tmuntan1

Member

Registered: 2014-11-14

Posts: 6

Re: Update Problems with filesystem

Thanks for your help, but it's the end of my workday and I am going to leave this problem for Monday to solve.

karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: Update Problems with filesystem

You can use your backup, if you have one.
IIRC '--force' will overwrite files that should be backed up.