Can't Update Because file "exists in filesystem" [SOLVED]

CaptainKirk · 2014-08-06 12:50:15

I am having the below problem:

$ sudo pacman -Suyy
:: Synchronizing package databases...
 core                                                     112.9 KiB  2.83M/s 00:00 [###############################################] 100%
 extra                                                   1763.2 KiB   845K/s 00:02 [###############################################] 100%
 community                                                  2.3 MiB  2.65M/s 00:01 [###############################################] 100%
 archlinuxfr                                               19.7 KiB   160K/s 00:00 [###############################################] 100%
:: Starting full system upgrade...
error: could not open file /var/lib/pacman/local/ldb-1.1.16-1/desc: No such file or directory
:: Replace lzo2 with core/lzo? [Y/n] 
resolving dependencies...
error: could not open file /var/lib/pacman/local/libgxps-0.2.2-3/desc: No such file or directory
looking for inter-conflicts...

Packages (43): cairo-1.12.16-3  cups-1.7.5-1  device-mapper-2.02.108-1  dhcpcd-6.4.3-1  e2fsprogs-1.42.11-1  epiphany-3.12.1-2
               ffmpeg-1:2.3.1-1  gettext-0.19.2-1  git-2.0.4-1  kdelibs-4.13.3-2  ldb-1.1.17-1  libarchive-3.1.2-8  libcups-1.7.5-1
               libkolab-0.5.2-1  libpeas-1.10.1-1  libutil-linux-2.25-3  libwbclient-4.1.11-1  linux-3.15.8-1  linux-headers-3.15.8-1
               lvm2-2.02.108-1  lzo-2.08-3  lzo2-2.08-1 [removal]  meld-3.11.2-3  mesa-10.2.5-1  mkinitcpio-18-1  parted-3.2-1
               phpmyadmin-4.2.7-1  python-setuptools-1:5.4.2-1  python2-boto-2.32.1-1  s-nail-14.7.5-1  samba-4.1.11-1
               smartmontools-6.3-1  smbclient-4.1.11-1  syslinux-6.03pre19-1  tar-1.28-1  tdb-1.3.0-2  traceroute-2.0.20-1
               util-linux-2.25-3  virtualbox-4.3.14-3  xorg-server-1.16.0-6  xorg-server-common-1.16.0-6  xorg-xrandr-1.4.3-1
               zenity-3.12.1-2

Total Installed Size:   450.30 MiB
Net Upgrade Size:       1.10 MiB

:: Proceed with installation? [Y/n] 
(42/42) checking keys in keyring                                                   [###############################################] 100%
(42/42) checking package integrity                                                 [###############################################] 100%
(42/42) loading package files                                                      [###############################################] 100%
(42/42) checking for file conflicts                                                [###############################################] 100%
error: failed to commit transaction (conflicting files)
ldb: /usr/bin/ldbadd exists in filesystem
ldb: /usr/bin/ldbdel exists in filesystem
ldb: /usr/bin/ldbedit exists in filesystem
ldb: /usr/bin/ldbmodify exists in filesystem
ldb: /usr/bin/ldbrename exists in filesystem
ldb: /usr/bin/ldbsearch exists in filesystem
ldb: /usr/include/ldb.h exists in filesystem
ldb: /usr/include/ldb_errors.h exists in filesystem
ldb: /usr/include/ldb_handlers.h exists in filesystem
ldb: /usr/include/ldb_module.h exists in filesystem
ldb: /usr/include/ldb_version.h exists in filesystem
ldb: /usr/include/pyldb.h exists in filesystem
ldb: /usr/lib/ldb/libldb-cmdline.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/asq.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/ldap.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/paged_results.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/paged_searches.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/rdn_name.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/sample.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/server_sort.so exists in filesystem
ldb: /usr/lib/ldb/modules/ldb/skel.so exists in filesystem
ldb: /usr/lib/libldb.so exists in filesystem
ldb: /usr/lib/libldb.so.1 exists in filesystem
ldb: /usr/lib/libpyldb-util.so exists in filesystem
ldb: /usr/lib/libpyldb-util.so.1 exists in filesystem
ldb: /usr/lib/pkgconfig/ldb.pc exists in filesystem
ldb: /usr/lib/pkgconfig/pyldb-util.pc exists in filesystem
ldb: /usr/lib/python2.7/site-packages/ldb.so exists in filesystem
Errors occurred, no packages were upgraded.

Recently I did have a problem with my pacman DB files over here but I fixed that. I also tried now making a new empty /var/lib/pacman/sync directory but the output is the same as above.

I tried Googling for this issue but I am not succeededing.

Can anyone advise what I can do to troubleshoot this?

Last edited by CaptainKirk (2014-08-07 11:28:01)

Trilby · 2014-08-06 13:36:57

I don't know what search terms you used that could have missed this:
https://wiki.archlinux.org/index.php/Pa … stem.22.21

That is also covered in a sticked forum thread.

Your title however is misleading - nothing says files are missing, the problem is those files are already there but pacman doesn't know why.

CaptainKirk · 2014-08-06 13:50:50

Thank you for that link.

I checked the first two /usr/bin/ldbadd and /usr/bin/ldbdel and no package owns them. So I ran:

sudo pacman -S --force lib32-libdbus

because now I got:

:: Replace lib32-dbus-core with multilib/lib32-libdbus? [Y/n]

because I just enabled multilib in order to upgrade skype (which worked). Anyhow, the install of lib32-libdbus worked fine, but

pacman -Syu

still gives all the errors above. Should I try to rename all those files?

Your title however is misleading - nothing says files are missing, the problem is those files are already there but pacman doesn't know why.

Well, I also see this:

error: could not open file /var/lib/pacman/local/ldb-1.1.16-1/desc: No such file or directory

as well as another. So something does appear to be missing to me.

karol · 2014-08-06 16:36:14

This means your local package database got corrupted.
How exactly did you check if these files are owned by a package or not?

$ pkgfile /usr/bin/ldbdel
extra/ldb

'pacman -Qo' may not work if your local package database is busted.

falconindy · 2014-08-06 17:20:29

CaptainKirk wrote:

So something does appear to be missing to me.

But the missing desc files aren't what cause pacman to fail to install the file, hence the mention that your topic is inaccurate.

CaptainKirk · 2014-08-06 18:44:07

karol, yes I had used 'pacman -Qo' and pkgfile indeed gives the same output as you.

How do I uncorrupt my package databases? I removed the directory /var/lib/pacman/sync today and made a fresh empty one and ran pacman -Syy to refresh it, but that was before I ever posted.

I think this may be the real issue....

Because, falconindy, even if you are correct (which I presume you are) that the missing files are not the problem to install, they are still a problem. How do I fix that?

karol · 2014-08-06 21:54:36

I'm not talking about the sync dbs, but your local db - /var/lib/pacman/local .
Have you tried installing ldb with '--force'?

CaptainKirk · 2014-08-07 11:27:49

I changed the topic of this thread.

karol, I had tried that before, but it failed. Seems now that I enabled multilib, it worked!

Everything seems fine now.

Thank you very much!

bkz7abc · 2018-09-24 08:53:48

I have solved:
sudo pacman -S --force python2-setuptools

WorMzy · 2018-09-24 11:34:13

Please don't necrobump: https://wiki.archlinux.org/index.php/Co … bumping.22

Closing.

Arch Linux

#1 2014-08-06 12:50:15

Can't Update Because file "exists in filesystem" [SOLVED]

#2 2014-08-06 13:36:57

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#3 2014-08-06 13:50:50

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#4 2014-08-06 16:36:14

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#5 2014-08-06 17:20:29

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#6 2014-08-06 18:44:07

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#7 2014-08-06 21:54:36

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#8 2014-08-07 11:27:49

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#9 2018-09-24 08:53:48

Re: Can't Update Because file "exists in filesystem" [SOLVED]

#10 2018-09-24 11:34:13

Re: Can't Update Because file "exists in filesystem" [SOLVED]

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