glibc /lib errors

[ruidc]

I got the following today - having been up-to-date yesterday:
$this->bbcode_second_pass_code('', 'error: failed to commit transaction (conflicting files)
glibc: /lib exists in filesystem
Errors occurred, no packages were upgraded.')

am running 2.16.0-1 upgrading to 2.16.0-4.

having followed the instructions here: https://wiki.archlinux.org/index.php/De ... iki:usrlib

when running:
$this->bbcode_second_pass_code('', 'grep '^lib/' /var/lib/pacman/local/*/files')

I get:
$this->bbcode_second_pass_code('', '
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/ld-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/ld-linux.so.3
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libBrokenLocale-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libBrokenLocale.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libSegFault.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libanl-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libanl.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libc-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libc.so.6
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcidn-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcidn.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcrypt-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcrypt.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libdl-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libdl.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libm-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libm.so.6
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libmemusage.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnsl-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnsl.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_compat-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_compat.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_db-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_db.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_dns-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_dns.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_files-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_files.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_hesiod-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_hesiod.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nis-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nis.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nisplus-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nisplus.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libpcprofile.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libpthread-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libpthread.so.0
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libresolv-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libresolv.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/librt-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/librt.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libthread_db-1.0.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libthread_db.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libutil-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libutil.so.1
/var/lib/pacman/local/pcmciautils-017-1/files:lib/
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/pcmcia-check-broken-cis
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/pcmcia-socket-startup
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/rules.d/
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/rules.d/60-pcmcia.rules

')

Can anyone offer assistance?

[pepedog]

Can you try pacman -Syu again please

[ruidc]

same - and it's not picking up any further updates in the repo

[pepedog]

I can't help much. My v6 install went fine on update. Also pure systemd now boots in 8 seconds

[ruidc]

good stuff!, ok, for now i'll just ignore glibc

[slycat]

so pure systemd setups don't need to ignore glibc, but us initscript folk do?
If this is the case, I'll bite the bullet and start the switch. Just no time to figure out all of systemd yet.

[pepedog]

$this->bbcode_second_pass_quote('slycat', 's')o pure systemd setups don't need to ignore glibc, but us initscript folk do?
If this is the case, I'll bite the bullet and start the switch. Just no time to figure out all of systemd yet.

[pepedog]

Winfried posted a soloution here
http://www.raspberrypi.org/phpBB3/viewt ... 70#p174336
$this->bbcode_second_pass_quote('winfried', 'H')i,

I followed instructions from here
http://www.cidtux.com/1/post/2012/7/solve-lib-exists-in-filesystem-on-archlinux-upgrade.html
and the good new is -- it works perfect.

$this->bbcode_second_pass_code('', '
[root@alarmpi ~]# rm -r /lib/modules/
[root@alarmpi ~]# rm -r /lib/udev/
[root@alarmpi ~]# pacman -Syu
:: Synchronizing package databases...
core is up to date
extra is up to date
community is up to date
alarm is up to date
aur is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Targets (7): filesystem-2012.8-1 glibc-2.16.0-4 initscripts-2012.08.3-2 kmod-10-1
linux-raspberrypi-3.2.27-5 raspberrypi-firmware-20120914-1 syslog-ng-3.3.6-1

Total Download Size: 30.11 MiB
Total Installed Size: 89.79 MiB
Net Upgrade Size: 0.69 MiB

Proceed with installation? [Y/n] Y
:: Retrieving packages from core...
filesystem-2012.8-1-any 5.8 KiB 35.1K/s 00:00 [##################################] 100%
glibc-2.16.0-4-arm 7.6 MiB 86.4K/s 01:30 [##################################] 100%
initscripts-2012.08.3-2-any 23.1 KiB 38.9K/s 00:01 [##################################] 100%
kmod-10-1-arm 85.8 KiB 78.0K/s 00:01 [##################################] 100%
linux-raspberrypi-3.2.27-5-arm 12.3 MiB 83.5K/s 02:31 [##################################] 100%
syslog-ng-3.3.6-1-arm 299.4 KiB 88.7K/s 00:03 [##################################] 100%
:: Retrieving packages from alarm...
raspberrypi-firmware-20120914-... 9.8 MiB 85.2K/s 01:58 [##################################] 100%
(7/7) checking package integrity [##################################] 100%
(7/7) loading package files [##################################] 100%
(7/7) checking for file conflicts [##################################] 100%
error: failed to commit transaction (conflicting files)
glibc: /lib exists in filesystem
Errors occurred, no packages were upgraded.

[root@alarmpi ~]# pacman -Su --ignore glibc
:: Starting full system upgrade...
warning: glibc: ignoring package upgrade (2.16.0-1 => 2.16.0-4)
resolving dependencies...
looking for inter-conflicts...

Targets (6): filesystem-2012.8-1 initscripts-2012.08.3-2 kmod-10-1 linux-raspberrypi-3.2.27-5
raspberrypi-firmware-20120914-1 syslog-ng-3.3.6-1

Total Installed Size: 56.05 MiB
Net Upgrade Size: 0.59 MiB

Proceed with installation? [Y/n] Y
(6/6) checking package integrity [##################################] 100%
(6/6) loading package files [##################################] 100%
(6/6) checking for file conflicts [##################################] 100%
(6/6) checking available disk space [##################################] 100%
(1/6) upgrading filesystem [##################################] 100%
warning: directory permissions differ on sys/
filesystem: 755 package: 555
(2/6) upgrading initscripts [##################################] 100%
----
> initscripts now ships a compatibility layer to make systemd use MODULES and
> DAEMONS from rc.conf; and run rc.local and rc.local.shutdown on boot and
> shutdown, respectively. Refer to arch-modules-load(8) and arch-daemons(8).
----
New optional dependencies for initscripts
bridge-utils: Legacy network bridging support
net-tools: Legacy network support
wireless_tools: Legacy wireless networking
(3/6) upgrading kmod [##################################] 100%
(4/6) upgrading linux-raspberrypi [##################################] 100%
>>> Updating module dependencies. Please wait ...
ERROR: could not open directory /lib/modules/3.2.27-5-ARCH+: No such file or directory
FATAL: could not search modules: No such file or directory
error: command failed to execute correctly
>>>Current installed start.elf: /boot/arm224_start.elf
(5/6) upgrading raspberrypi-firmware [##################################] 100%
>>>Replacing /boot/start.elf with /boot/arm224_start.elf
(6/6) upgrading syslog-ng [##################################] 100%
[root@alarmpi ~]#

[root@alarmpi ~]# grep '^lib/' /var/lib/pacman/local/*/files | grep -v glibc
/var/lib/pacman/local/pcmciautils-017-1/files:lib/
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/pcmcia-check-broken-cis
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/pcmcia-socket-startup
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/rules.d/
/var/lib/pacman/local/pcmciautils-017-1/files:lib/udev/rules.d/60-pcmcia.rules
[root@alarmpi ~]# rm -r /var/lib/pacman/local/pcmciautils-017-1/
[root@alarmpi ~]# grep '^lib/' /var/lib/pacman/local/*/files | grep -v glibc
[root@alarmpi ~]# find /lib -exec pacman -Qo -- {} +
error: cannot determine ownership of directory '/lib'
/lib/libnss_db.so.2 is owned by glibc 2.16.0-1
/lib/libmemusage.so is owned by glibc 2.16.0-1
/lib/libnss_dns.so.2 is owned by glibc 2.16.0-1
/lib/libnss_nisplus-2.16.so is owned by glibc 2.16.0-1
/lib/ld-2.16.so is owned by glibc 2.16.0-1
/lib/ld-linux.so.3 is owned by glibc 2.16.0-1
/lib/libpcprofile.so is owned by glibc 2.16.0-1
/lib/libnss_compat-2.16.so is owned by glibc 2.16.0-1
/lib/libc.so.6 is owned by glibc 2.16.0-1
/lib/libc-2.16.so is owned by glibc 2.16.0-1
/lib/libnss_db-2.16.so is owned by glibc 2.16.0-1
/lib/libcidn.so.1 is owned by glibc 2.16.0-1
/lib/libcidn-2.16.so is owned by glibc 2.16.0-1
/lib/libnss_hesiod.so.2 is owned by glibc 2.16.0-1
/lib/libnss_nisplus.so.2 is owned by glibc 2.16.0-1
/lib/libnss_nis-2.16.so is owned by glibc 2.16.0-1
/lib/libutil.so.1 is owned by glibc 2.16.0-1
/lib/libnss_files.so.2 is owned by glibc 2.16.0-1
/lib/libdl.so.2 is owned by glibc 2.16.0-1
/lib/libanl.so.1 is owned by glibc 2.16.0-1
/lib/libpthread.so.0 is owned by glibc 2.16.0-1
/lib/libanl-2.16.so is owned by glibc 2.16.0-1
/lib/libBrokenLocale-2.16.so is owned by glibc 2.16.0-1
/lib/libnss_dns-2.16.so is owned by glibc 2.16.0-1
/lib/libnsl-2.16.so is owned by glibc 2.16.0-1
/lib/libSegFault.so is owned by glibc 2.16.0-1
/lib/libutil-2.16.so is owned by glibc 2.16.0-1
/lib/libthread_db.so.1 is owned by glibc 2.16.0-1
/lib/libresolv.so.2 is owned by glibc 2.16.0-1
/lib/libnss_files-2.16.so is owned by glibc 2.16.0-1
/lib/libBrokenLocale.so.1 is owned by glibc 2.16.0-1
/lib/libdl-2.16.so is owned by glibc 2.16.0-1
/lib/librt.so.1 is owned by glibc 2.16.0-1
/lib/libthread_db-1.0.so is owned by glibc 2.16.0-1
/lib/libnss_compat.so.2 is owned by glibc 2.16.0-1
/lib/librt-2.16.so is owned by glibc 2.16.0-1
/lib/libnss_hesiod-2.16.so is owned by glibc 2.16.0-1
/lib/libnss_nis.so.2 is owned by glibc 2.16.0-1
/lib/libcrypt-2.16.so is owned by glibc 2.16.0-1
/lib/libcrypt.so.1 is owned by glibc 2.16.0-1
/lib/libm-2.16.so is owned by glibc 2.16.0-1
/lib/libresolv-2.16.so is owned by glibc 2.16.0-1
/lib/libnsl.so.1 is owned by glibc 2.16.0-1
/lib/libm.so.6 is owned by glibc 2.16.0-1
/lib/libpthread-2.16.so is owned by glibc 2.16.0-1
[root@alarmpi ~]#

[root@alarmpi ~]# pacman -Su
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Targets (1): glibc-2.16.0-4

Total Installed Size: 33.75 MiB
Net Upgrade Size: 0.10 MiB

Proceed with installation? [Y/n] Y
(1/1) checking package integrity [##################################] 100%
(1/1) loading package files [##################################] 100%
(1/1) checking for file conflicts [##################################] 100%
(1/1) checking available disk space [##################################] 100%
(1/1) upgrading glibc [##################################] 100%
Generating locales...
en_US.UTF-8... done
en_US.ISO-8859-1... done
de_DE.ISO-8859-1... done
de_DE.ISO-8859-15@euro... done
Generation complete.
')

Winfried

[karog]

@ruidc, the output of the grep shows that you have the package pcmciautils installed and that is what is causing the problem. You need to remove it with
$this->bbcode_second_pass_code('', '
pacman -R pcmciautils')
Then the glibc will update properly.

On pogo V3's, you also need to remove the packages kernel26-oxnas-nopci and kernel26-oxnas-pci. You also need to move /lib/firmware/gmac_copro_firmware to /usr/lib/firmware and rm -r /lib/firmware (after making sure it is empty).

[ruidc]

thanks karog, but must be something else there too:

$this->bbcode_second_pass_code('', '
[root@alarm ~]# pacman -R pcmciautils
checking dependencies...

Targets (1): pcmciautils-017-1

Total Removed Size: 0.09 MiB

Do you want to remove these packages? [Y/n] y
(1/1) removing pcmciautils [######################] 100%
[root@alarm ~]# pacman -Syu --ignore mediatomb
:: Synchronising package databases...
core 38.1 KiB 111K/s 00:00 [######################] 100%
extra 430.1 KiB 523K/s 00:01 [######################] 100%
community 420.4 KiB 1080K/s 00:00 [######################] 100%
alarm 4.6 KiB 3.59M/s 00:00 [######################] 100%
aur 11.8 KiB 6.24M/s 00:00 [######################] 100%
:: Starting full system upgrade...
warning: mediatomb: local (0.12.1-8.2) is newer than aur (0.12.1-8)
resolving dependencies...
looking for inter-conflicts...

Targets (1): glibc-2.16.0-4

Total Installed Size: 33.75 MiB
Net Upgrade Size: 0.10 MiB

Proceed with installation? [Y/n] y
(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)
glibc: /lib exists in filesystem
Errors occurred, no packages were upgraded.
[root@alarm ~]# grep '^lib/' /var/lib/pacman/local/*/files
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/ld-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/ld-linux.so.3
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libBrokenLocale-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libBrokenLocale.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libSegFault.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libanl-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libanl.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libc-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libc.so.6
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcidn-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcidn.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcrypt-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libcrypt.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libdl-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libdl.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libm-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libm.so.6
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libmemusage.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnsl-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnsl.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_compat-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_compat.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_db-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_db.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_dns-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_dns.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_files-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_files.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_hesiod-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_hesiod.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nis-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nis.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nisplus-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libnss_nisplus.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libpcprofile.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libpthread-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libpthread.so.0
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libresolv-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libresolv.so.2
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/librt-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/librt.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libthread_db-1.0.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libthread_db.so.1
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libutil-2.16.so
/var/lib/pacman/local/glibc-2.16.0-1/files:lib/libutil.so.1
[root@alarm ~]#

')

I have systemd installed but haven't yet converted - too chicken - will wait a bit first.