[How-To] pacman fails to upgrade glibc (glibc: /lib exists)

[slycat]

pepedog, thanks for that workaround but I've got it all working again. Also, since the modules were moved to /usr/lib before removing the packages I still have my 2.6.31 and 3.10 modules (good thing, kernel26-oxnas-pci isn't in the repo and I didn't wanna have to dig into a backup to grab it again).

WHSE, thanks for trying to keep things up to date and all, but personally I don't wanna start fresh again >.< too many edits to keep track of, unless the new setup with be pure systemd but seriously, thanks for all the support on the oxnas.

[BillyBoy]

@Admins:

Could you please make this thread sticky, as this issue still exists, especially for NEW installations!
Thanks a lot.

[francois]

Hi all,

first of all, sorry for my English, I'm just a poor french guy

My device is a Seagate Dockstar.

I followed all the instructions but I'm falling again and again on the same error when I try a $this->bbcode_second_pass_code('', 'pacman -Suy') :

$this->bbcode_second_pass_code('', 'Synchronizing package databases...
core 38.9 KiB 220K/s 00:00 [#######################] 100%
extra is up to date
community is up to date
alarm is up to date
aur is up to date
:: The following packages should be upgraded first :
pacman
:: Do you want to cancel the current operation
:: and upgrade these packages now? [Y/n] y

resolving dependencies...
looking for inter-conflicts...
:: gnupg and gnupg2 are in conflict. Remove gnupg2? [y/N] y

Targets (21): ca-certificates-20121105-1 coreutils-8.20-1 curl-7.28.1-1
db-5.3.21-1 dirmngr-1.1.0-4 e2fsprogs-1.42.6-1 gcc-libs-4.7.2-2
gmp-5.1.0-1 gnupg-2.0.19-3 gnupg2-2.0.18-1 [removal]
gpgme-1.3.1-4 libarchive-3.0.4-2 libldap-2.4.33-3
libssh2-1.4.3-1 openssl-1.0.1.c-1 pam-1.1.6-1
pambase-20120701-1 perl-5.16.2-2 shadow-4.1.5.1-2
util-linux-2.22.2-1 pacman-4.0.3-5

Total Installed Size: 123.88 MiB
Net Upgrade Size: -3.99 MiB

Proceed with installation? [Y/n] y
(20/20) checking package integrity [#######################] 100%
(20/20) loading package files [#######################] 100%
(20/20) checking for file conflicts [#######################] 100%
error: failed to commit transaction (conflicting files)
util-linux: /sbin/sulogin exists in filesystem
util-linux: /usr/bin/mesg exists in filesystem
util-linux: /usr/bin/utmpdump exists in filesystem
util-linux: /usr/bin/wall exists in filesystem
util-linux: /usr/share/man/man1/mesg.1.gz exists in filesystem
util-linux: /usr/share/man/man1/utmpdump.1.gz exists in filesystem
util-linux: /usr/share/man/man1/wall.1.gz exists in filesystem
util-linux: /usr/share/man/man8/sulogin.8.gz exists in filesystem
Errors occurred, no packages were upgraded.
')


I don't know what to do (I'm not very experienced with Linux)

Is there a way for one of you to help me please?

[pepedog]

Find out who owns the files, eg
$this->bbcode_second_pass_code('', 'pacman -Qo /sbin/sulogin')
Mine shows util-linux which is not surprising, but yours must be different
You could always force with pacman -Sf util-linux but best to find out if those files are owned first

[francois]

Thanks for your answer!

I've juste tried a

$this->bbcode_second_pass_code('', 'pacman -Syuf')

which returns :

$this->bbcode_second_pass_code('', '[root@alarm /]# pacman -Syuf
:: 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
:: The following packages should be upgraded first :
pacman
:: Do you want to cancel the current operation
:: and upgrade these packages now? [Y/n] [b]n[/b]

:: Starting full system upgrade...
:: Replace dbus-core with core/dbus? [Y/n] [b]y[/b]
:: Replace gnupg2 with core/gnupg? [Y/n] [b]y[/b]
:: Replace udev with core/systemd? [Y/n] [b]y[/b]

resolving dependencies...
looking for inter-conflicts...

Targets (66): audiofile-0.3.4-1 binutils-2.23-1 ca-certificates-20121105-1
cifs-utils-5.8-1 coreutils-8.20-1 cronie-1.4.9-1
cryptsetup-1.5.1-1 curl-7.28.1-1 db-5.3.21-1 dbus-1.6.8-6
dbus-core-1.4.16-1 [removal] device-mapper-2.02.98-1
dirmngr-1.1.0-4 dnssec-anchors-20120422-1 e2fsprogs-1.42.6-1
ffmpeg-1:1.0.1-1 filesystem-2012.12-1 glib2-2.34.3-1
gmp-5.1.0-1 gnupg-2.0.19-3 gnupg2-2.0.18-1 [removal]
gpgme-1.3.1-4 grep-2.14-1 inetutils-1.9.1-4
initscripts-2012.10.1-1 iproute2-3.6.0-2 iptables-1.4.16.2-1
iputils-20121126-1 khrplatform-devel-9.0.1-1 krb5-1.11-1
ldns-1.6.16-1 less-451-1 libarchive-3.0.4-2 libegl-9.0.1-1
libgbm-9.0.1-1 libgl-9.0.1-1 libldap-2.4.33-3 libpulse-3.0-2
libssh2-1.4.3-1 libva-1.1.0-2 linux-3.1.10-15 logrotate-3.8.2-2
lvm2-2.02.98-1 mkinitcpio-0.12.0-2 mpd-0.17.2-1
nss-myhostname-0.3-3 openssh-6.1p1-4 openssl-1.0.1.c-1
pacman-4.0.3-5 pam-1.1.6-1 pambase-20120701-1 pcre-8.32-1
perl-5.16.2-2 rtmpdump-20121203-1 shadow-4.1.5.1-2
syslog-ng-3.3.7-1 systemd-196-2 sysvinit-2.88-9
sysvinit-tools-2.88-9 udev-181-5 [removal] util-linux-2.22.2-1
v4l-utils-0.8.9-1 wget-1.14-2 wpa_supplicant-1.0-2
xfsprogs-3.1.8-2 yajl-2.0.4-1

Total Installed Size: 262.29 MiB
Net Upgrade Size: 31.46 MiB

Proceed with installation? [Y/n] y
(63/63) checking package integrity [#######################] 100%
(63/63) loading package files [#######################] 100%
(66/66) checking available disk space [#######################] 100%
(1/3) removing dbus-core [#######################] 100%
usr/sbin/userdel: error while loading shared libraries: libpam.so.0: cannot open shared object file: No such file or directory
usr/sbin/groupdel: error while loading shared libraries: libpam.so.0: cannot open shared object file: No such file or directory
error: command failed to execute correctly
(2/3) removing udev [#######################] 100%
(3/3) removing gnupg2 [#######################] 100%
( 1/63) upgrading audiofile [#######################] 100%
( 2/63) upgrading binutils [#######################] 100%
( 3/63) upgrading db [#######################] 100%
( 4/63) installing pambase [#######################] 100%
( 5/63) upgrading pam [#######################] 100%
( 6/63) upgrading gmp [#######################] 100%
( 7/63) upgrading coreutils [#######################] 100%
( 8/63) upgrading perl [#######################] 100%
( 9/63) upgrading openssl [#######################] 100%
(10/63) upgrading ca-certificates [#######################] 100%
(11/63) upgrading shadow [#######################] 100%
(12/63) upgrading util-linux [#######################] 100%
(13/63) upgrading e2fsprogs [#######################] 100%
(14/63) upgrading libldap [#######################] 100%
(15/63) upgrading krb5 [#######################] 100%
(16/63) upgrading cifs-utils [#######################] 100%
(17/63) upgrading cronie [#######################] 100%
New optional dependencies for cronie
pm-utils: defer anacron when on battery power
(18/63) installing nss-myhostname [#######################] 100%
(19/63) upgrading filesystem [#######################] 100%
warning: /etc/group installed as /etc/group.pacnew
warning: /etc/shadow installed as /etc/shadow.pacnew
warning: /etc/passwd installed as /etc/passwd.pacnew
warning: /etc/gshadow installed as /etc/gshadow.pacnew
warning: directory permissions differ on sys/
filesystem: 755 package: 555
(20/63) upgrading dbus [#######################] 100%
New optional dependencies for dbus
libx11: dbus-launch support
(21/63) upgrading pcre [#######################] 100%
(22/63) upgrading glib2 [#######################] 100%
(23/63) installing systemd [#######################] 100%
Initializing machine ID from D-Bus machine ID.
==> Warning: setcap failed, falling back to setuid root on /usr/bin/systemd-detect-virt
ln -s '/usr/lib/systemd/system/getty@.service' '/etc/systemd/system/getty.target.wants/getty@tty1.service'
:: Append 'init=/bin/systemd' to your kernel command line in your
bootloader to replace sysvinit with systemd
Optional dependencies for systemd
cryptsetup: required for encrypted block devices
libmicrohttpd: systemd-journal-gatewayd
quota-tools: kernel-level quota management
python: systemd library bindings
python2-cairo: systemd-analyze
python2-gobject: systemd-analyze
systemd-sysvcompat: symlink package to provide sysvinit binaries
(24/63) upgrading device-mapper [#######################] 100%
(25/63) upgrading cryptsetup [#######################] 100%
(26/63) upgrading libssh2 [#######################] 100%
(27/63) upgrading curl [#######################] 100%
(28/63) upgrading dirmngr [#######################] 100%
(29/63) upgrading libpulse [#######################] 100%
(30/63) installing libgbm [#######################] 100%
(31/63) installing khrplatform-devel [#######################] 100%
(32/63) installing libegl [#######################] 100%
(33/63) upgrading libgl [#######################] 100%
(34/63) upgrading libva [#######################] 100%
New optional dependencies for libva
libva-intel-driver: back-end for intel cards
libva-vdpau-driver: vdpau back-end for nvidia
(35/63) upgrading rtmpdump [#######################] 100%
(36/63) installing v4l-utils [#######################] 100%
Optional dependencies for v4l-utils
qt
(37/63) upgrading ffmpeg [#######################] 100%
(38/63) upgrading gnupg [#######################] 100%
New optional dependencies for gnupg
curl: gpg2keys_curl
libldap: gpg2keys_ldap
libusb-compat: scdaemon
(39/63) upgrading gpgme [#######################] 100%
(40/63) upgrading grep [#######################] 100%
(41/63) upgrading inetutils [#######################] 100%
(42/63) installing iptables [#######################] 100%
(43/63) upgrading iproute2 [#######################] 100%
(44/63) installing sysvinit-tools [#######################] 100%
(45/63) upgrading initscripts [#######################] 100%
----
> initscripts now ships a compatibility layer to make systemd use 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).
----
----
> systemd no longer reads MODULES from rc.conf.
----
New optional dependencies for initscripts
bridge-utils: Legacy network bridging support
net-tools: Legacy network support
sysvinit: Legacy init support
wireless_tools: Legacy wireless networking
(46/63) upgrading iputils [#######################] 100%
New optional dependencies for iputils
xinetd: for tftpd
(47/63) upgrading less [#######################] 100%
(48/63) upgrading libarchive [#######################] 100%
(49/63) upgrading mkinitcpio [#######################] 100%
==> If your /usr is on a separate partition, you must add the "usr" hook
to /etc/mkinitcpio.conf and regenerate your images before rebooting
==> The "block" hook has replaced several hooks:
fw, sata, pata, scsi, virtio, mmc, usb
Replace any and all of these in /etc/mkinitcpio.conf with a single
instance of the "block" hook
(50/63) upgrading linux [#######################] 100%
>>> Updating module dependencies. Please wait ...
(51/63) upgrading logrotate [#######################] 100%
New optional dependencies for logrotate
cron: scheduled log rotation
(52/63) upgrading lvm2 [#######################] 100%
(53/63) installing yajl [#######################] 100%
(54/63) upgrading mpd [#######################] 100%
warning: /etc/mpd.conf installed as /etc/mpd.conf.pacnew
(55/63) installing dnssec-anchors [#######################] 100%
(56/63) installing ldns [#######################] 100%
Optional dependencies for ldns
libpcap: ldns-dpa tool
(57/63) upgrading openssh [#######################] 100%
New optional dependencies for openssh
x11-ssh-askpass: input passphrase in X
xorg-xauth: X11 forwarding
(58/63) upgrading pacman [#######################] 100%
>>> Run `pacman-key --init` to set up your pacman keyring.
(59/63) upgrading syslog-ng [#######################] 100%
==> syslog-ng now reads from /run/systemd/journal/syslog in the
default config. If you still use sysvinit/initscripts, this
must be /dev/log in /etc/syslog-ng/syslog-ng.conf
(60/63) upgrading sysvinit [#######################] 100%
(61/63) upgrading wget [#######################] 100%
(62/63) upgrading wpa_supplicant [#######################] 100%
(63/63) upgrading xfsprogs [#######################] 100%
')

It seems that everything was upgraded but

when I try :

$this->bbcode_second_pass_code('', 'pacman -Qo /sbin/sulogin
error: failed to read file '/sbin/sulogin': No such file or directory')

Maybe it would be better that I open a dedicated thread? And not trying anything else without your advice

[pepedog]

You were lucky there, you was supposed to find out who owns the file first, then force the one package
Is util-linux now installed?

[francois]

$this->bbcode_second_pass_quote('pepedog', 'I')s util-linux now installed?

[pepedog]

pacman -S util-linux

[karog]

To install: pacman -S util-linux

To check if installed: pacman -Q util-linux