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#1 2016-03-13 12:45:33

PeterBell
Member
Registered: 2014-07-20
Posts: 39

[Solved]Lots of authentication issues since pacman -Syu today

I'm running the Cinnamon desktop with LightDM.  Since performing a full sustem upgrade earlier, I am getting lots of errors/failures to run.

Edit to add solution:
Creating a fairly standard local .xinitrc file (where there was none previously) appears to have resolved the issue.
Apparently untrue!  Removing (or renaming) the .xinitrc does not cause the failure to recur.

For instance, launching unetbootin from the Menu results in an error:

Error executing command as another user: No authentication agent found.

Launching GParted from the menu results in an hour glass for about 10 seconds, but gparted window doesn't open.
Running "sudo gparted" from a terminal results in a lengthy pause followed by the error:

Failed to list units: Connection timed out

, but a gparted window does open.

Plugging in a USB memory stick results in an error window:

Not authorized to perform operation

Attempting to identify any system processes having failed to start, I tried to run systemctl from a terminal.  After a 15-20 second delay, the only result is the same error messge as gparted:

Failed to list units: Connection timed out

Logging in to the desktop seems to take much longer than it used to.  I have performed several reboots with no improvement.

Googling suggests that this might be something to do with polkit being absent, but I understand that Cinnamon is one of the desktops which installs a polkit by default.

Can anyone suggest what might have gone wrong, how to pinpoint the problem and how to fix it?

Last edited by PeterBell (2016-03-14 15:37:51)

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#2 2016-03-13 12:49:57

Trilby
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Re: [Solved]Lots of authentication issues since pacman -Syu today

What was updated?  Is polkit installed?  Was polkit updated?


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#3 2016-03-13 14:49:27

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

Thanks for your reply!

The pacman log entries:

[2016-03-13 10:27] [PACMAN] Running 'pacman -Syu'
[2016-03-13 10:27] [PACMAN] synchronizing package lists
[2016-03-13 10:27] [PACMAN] starting full system upgrade
[2016-03-13 10:35] [ALPM] transaction started
[2016-03-13 10:35] [ALPM] upgraded perl (5.22.1-1 -> 5.22.1-2)
[2016-03-13 10:35] [ALPM] upgraded bind-tools (9.10.3.P3-3 -> 9.10.3.P4-1)
[2016-03-13 10:35] [ALPM] upgraded hwids (20150717-1 -> 20160306-1)
[2016-03-13 10:35] [ALPM] upgraded pcre (8.38-2 -> 8.38-3)
[2016-03-13 10:35] [ALPM] upgraded device-mapper (2.02.144-1 -> 2.02.145-1)
[2016-03-13 10:35] [ALPM] upgraded gtk-update-icon-cache (3.18.8-1 -> 3.18.9-1)
[2016-03-13 10:35] [ALPM] upgraded flashplugin (11.2.202.569-1 -> 11.2.202.577-1)
[2016-03-13 10:35] [ALPM] upgraded git (2.7.2-2 -> 2.7.3-1)
[2016-03-13 10:35] [ALPM] upgraded gtk3 (3.18.8-1 -> 3.18.9-1)
[2016-03-13 10:35] [ALPM] upgraded tevent (0.9.26-1 -> 0.9.28-1)
[2016-03-13 10:35] [ALPM] upgraded ldb (1.1.24-1 -> 1.1.26-1)
[2016-03-13 10:35] [ALPM] upgraded videoproto (2.3.2-1 -> 2.3.3-1)
[2016-03-13 10:35] [ALPM] upgraded libreoffice-fresh (5.1.0-2 -> 5.1.1-1)
[2016-03-13 10:35] [ALPM] upgraded libwbclient (4.3.5-1 -> 4.3.6-1)
[2016-03-13 10:35] [ALPM] upgraded linux (4.4.3-1 -> 4.4.5-1)
[2016-03-13 10:35] [ALPM-SCRIPTLET] >>> Updating module dependencies. Please wait ...
[2016-03-13 10:35] [ALPM-SCRIPTLET] >>> Generating initial ramdisk, using mkinitcpio. Please wait...
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Starting build: 4.4.5-1-ARCH
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [base]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [udev]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [autodetect]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [modconf]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [filesystems]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [keyboard]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [fsck]
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux.img
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Image generation successful
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Starting build: 4.4.5-1-ARCH
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [base]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [udev]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [modconf]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: wd719x
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: aic94xx
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [filesystems]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [keyboard]
[2016-03-13 10:35] [ALPM-SCRIPTLET]   -> Running build hook: [fsck]
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux-fallback.img
[2016-03-13 10:35] [ALPM-SCRIPTLET] ==> Image generation successful
[2016-03-13 10:35] [ALPM] upgraded thin-provisioning-tools (0.6.0-2 -> 0.6.1-2)
[2016-03-13 10:35] [ALPM] upgraded lvm2 (2.02.144-1 -> 2.02.145-1)
[2016-03-13 10:35] [ALPM] upgraded openssh (7.2p1-1 -> 7.2p2-1)
[2016-03-13 10:35] [ALPM] warning: /etc/pacman.d/mirrorlist installed as /etc/pacman.d/mirrorlist.pacnew
[2016-03-13 10:35] [ALPM] upgraded pacman-mirrorlist (20160227-1 -> 20160310-5)
[2016-03-13 10:35] [ALPM] upgraded python2-enum34 (1.1.1-1 -> 1.1.2-1)
[2016-03-13 10:35] [ALPM] upgraded sip (4.16.9-2 -> 4.17-1)
[2016-03-13 10:35] [ALPM] upgraded python2-sip (4.16.9-2 -> 4.17-1)
[2016-03-13 10:35] [ALPM] upgraded smbclient (4.3.5-1 -> 4.3.6-1)
[2016-03-13 10:35] [ALPM] upgraded samba (4.3.5-1 -> 4.3.6-1)
[2016-03-13 10:35] [ALPM] upgraded vim-runtime (7.4.1386-1 -> 7.4.1529-1)
[2016-03-13 10:35] [ALPM] upgraded vim (7.4.1386-1 -> 7.4.1529-1)
[2016-03-13 10:35] [ALPM] upgraded zeromq (4.1.3-4 -> 4.1.4-1)
[2016-03-13 10:35] [ALPM] transaction completed

I can't find polkit in there.

How can I prove whether polkit is installed?  I can find these files:

[peter@desktop ~]$ sudo find / -name polki*
[sudo] password for peter: 
find: ‘/home/peter/.gvfs’: Permission denied
/var/lib/pacman/local/polkit-0.113-4
/var/lib/pacman/local/polkit-gnome-0.105-3
/var/lib/pacman/local/polkit-qt4-0.112.0-3
/var/lib/pacman/local/polkit-qt5-0.112.0-3
find: ‘/run/user/1000/gvfs’: Permission denied
/etc/pam.d/polkit-1
/etc/polkit-1
/sys/fs/cgroup/pids/system.slice/polkit.service
/sys/fs/cgroup/devices/system.slice/polkit.service
/sys/fs/cgroup/systemd/system.slice/polkit.service

and this in my processes:

[peter@desktop ~]$ ps -eaf | grep pol
polkitd    457     1  0 14:50 ?        00:00:08 /usr/lib/polkit-1/polkitd --no-debug
peter      799     1  0 14:50 ?        00:00:00 [polkit-gnome-au] <defunct>
peter     8972  8094  0 22:45 pts/0    00:00:00 grep pol

The <defunct> looks a bit suspicious - what does that mean?

Last edited by PeterBell (2016-03-13 14:49:58)

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#4 2016-03-13 15:03:09

Trilby
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Registered: 2011-11-29
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Re: [Solved]Lots of authentication issues since pacman -Syu today

PeterBell wrote:

How can I prove whether polkit is installed?

pacman -Qs polkit

PeterBell wrote:

The <defunct> looks a bit suspicious - what does that mean?

I can't really help with that - I've never used polkit.  The output of the following might also be useful:

pacman -Q linux
uname -a
loginctl

"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#5 2016-03-13 15:16:02

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

I think that this indicates that polkit is installed?

[peter@desktop ~]$ pacman -Qs polkit
local/polkit 0.113-4
    Application development toolkit for controlling system-wide privileges
local/polkit-gnome 0.105-3
    Legacy polkit authentication agent for GNOME
local/polkit-qt4 0.112.0-3
    A library that allows developers to access PolicyKit API with a nice
    Qt-style API
local/polkit-qt5 0.112.0-3
    A library that allows developers to access PolicyKit API with a nice
    Qt-style API

... and the other commands:

[peter@desktop ~]$ pacman -Q linux
linux 4.4.5-1
[peter@desktop ~]$ uname -a
Linux desktop 4.4.5-1-ARCH #1 SMP PREEMPT Thu Mar 10 07:38:19 CET 2016 x86_64 GNU/Linux
[peter@desktop ~]$ loginctl
Failed to list sessions: Connection timed out
[peter@desktop ~]$ 

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#6 2016-03-13 15:36:08

Trilby
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Posts: 29,444
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Re: [Solved]Lots of authentication issues since pacman -Syu today

It looks like you don't have an active login which is likely the source of all the other problems.

Can you try temporarily disababling and stopping lightDM, then just log in to the tty and start X with startx (first creating an ~/.xinitrc if you don't have one).

If this works, then we'll know the problem is with lightDM which wouldn't be so surprising - Display Managers have been the source of countless problems lately.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#7 2016-03-13 15:48:14

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

Trilby wrote:

Can you try temporarily disababling and stopping lightDM

How can I do this?  I would normally expect to use systemctl - but that won't run.

Last edited by PeterBell (2016-03-13 15:53:05)

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#8 2016-03-13 16:05:31

Trilby
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Re: [Solved]Lots of authentication issues since pacman -Syu today

Ah, true.  If necessary, you can "rm" the releveant symlinks in the /etc/systemd, as that's all systemctl really does with disable/enable commands.  But a better approach would be to just boot to mutli-user.target by editing the kernel line in your boot loader.  This will prevent lightDM from ever starting during that boot up and you should get to a tty1 login prompt.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#9 2016-03-13 16:12:23

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

Okay, I can have a go at doing that.  However, in the meanwhile I have tried booting from the advanced options in the grub loader (AIUI, this boots with an older kernel - but what else does it change?).  Anyway, this appears to give me a fully operational system.

Last edited by PeterBell (2016-03-13 16:26:20)

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#10 2016-03-13 16:29:17

Trilby
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Re: [Solved]Lots of authentication issues since pacman -Syu today

I don't know what any of that means.  Why do you have an "older kernel" still installed.  Is this an lts kernel?  Otherwise this is generally not possible in arch.  Do you mean you used the "fallback kernel" which isn't actually a different kernel, just a different initramfs?

If this is just the fallback initramfs, something may have gone wrong in the initramfs build in the update and you should be able to rebuild it with `mkinitcpio -p linux`.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#11 2016-03-13 16:45:23

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

Sorry, I'm not quite sure what the 'Advanced options' in the grub menu actually do.  From experience with Ubuntu, I know that they offer alternative kernels - the description is less clear on my Arch installation.  I took an option "Arch Linux, with Linux linux" (not the fallback initramfs option).  But you are correct - it is running the same kernel (as reported by uname -a).

The only difference I can see between the default option and the 'Advanced' option which I took, is the gnulinux-simple and the gnulinux-linux-advanced in grub.cfg:

menuentry 'Arch Linux' --class arch --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-simple-89cfa1a2-025b-43c3-8b5c-5f47545031e2' {

and

menuentry 'Arch Linux, with Linux linux' --class arch --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-linux-advanced-89cfa1a2-025b-43c3-8b5c-5f47545031e2' {

If that difference is insignificant, then the only other change was that I had created a .xinitrc before I rebooted.

I'll try booting the default option again in a moment....

Edit to add
Yes, it appears that the significant change was the addition of .xinitrc.  Up until yesterday morning my system was running fine without a .xinitrc.  But, after the system update (with new kernel) it seems that .xinitrc became necessary for authentication to work properly.

I thank you for your time and patience - I wouldn't have resolved this issue without your assistance.

I will run for a while longer - make sure everything is really okay - before marking this topic as 'solved'.

Last edited by PeterBell (2016-03-13 16:58:07)

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#12 2016-03-13 16:48:47

ugjka
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From: Latvia
Registered: 2014-04-01
Posts: 1,794
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Re: [Solved]Lots of authentication issues since pacman -Syu today

Trilby wrote:

with startx (first creating an ~/.xinitrc if you don't have one).

You can do without xinitrc if you just wanna test stuff eg. startx /usr/bin/cinnamon-session


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#13 2016-03-13 17:57:11

jasonwryan
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From: .nz
Registered: 2009-05-09
Posts: 30,424
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Re: [Solved]Lots of authentication issues since pacman -Syu today

How did you install Arch?


Arch + dwm   •   Mercurial repos  •   Surfraw

Registered Linux User #482438

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#14 2016-03-13 18:11:00

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

jasonwryan wrote:

How did you install Arch?

From a bootable USB stick, and using pacstrap etc, but a long time ago.  Actually, maybe not that long ago - I had to replace the drive and I did a fresh install at that time.  Some of the system directories are dated Oct 1 - whether that would be the date of my install, or the date the distro image was created, I'm not exactly sure.

Ever since my original Arch Linux install, two or three years ago, I'd been using xfce, but I moved to Cinnamon just a couple of weeks back.

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#15 2016-03-14 04:48:48

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

Okay, I've been able to perform all the operations which I had reported as failing and I've rebooted a couple of times.  The boot completes as quickly as it did originally.

So, my conclusion is that something in the recent system update interfered with the authentication process to the point that it will not start unless .xinitrc is present.

Polkit is definitely enabled and starting now:

[peter@desktop ~]$ systemctl status polkit
● polkit.service - Authorization Manager
   Loaded: loaded (/usr/lib/systemd/system/polkit.service; static; vendor preset
   Active: active (running) since Mon 2016-03-14 01:35:32 PHT; 11h ago
     Docs: man:polkit(8)
 Main PID: 457 (polkitd)
    Tasks: 6 (limit: 512)
   CGroup: /system.slice/polkit.service
           └─457 /usr/lib/polkit-1/polkitd --no-debug

Mar 14 01:35:31 desktop systemd[1]: Starting Authorization Manager...
Mar 14 01:35:32 desktop polkitd[457]: Started polkitd version 0.113
Mar 14 01:35:32 desktop polkitd[457]: Loading rules from directory /etc/polkit-1
Mar 14 01:35:32 desktop polkitd[457]: Loading rules from directory /usr/share/po
Mar 14 01:35:32 desktop polkitd[457]: Finished loading, compiling and executing 
Mar 14 01:35:32 desktop systemd[1]: Started Authorization Manager.
Mar 14 01:35:32 desktop polkitd[457]: Acquired the name org.freedesktop.PolicyKi
Mar 14 01:35:54 desktop polkitd[457]: Registered Authentication Agent for unix-s

... and I no longer have a 'defunct' polkit process:

[peter@desktop ~]$ ps -eaf | grep pol
polkitd    457     1  0 01:35 ?        00:00:00 /usr/lib/polkit-1/polkitd --no-debug
peter      836   679  0 01:35 ?        00:00:00 /usr/lib/polkit-gnome/polkit-gnome-authentication-agent-1
peter     4312  3065  0 12:38 pts/0    00:00:00 grep pol

As for the .xinitrc file, I followed the recommendation in the wiki of making a local copy from the system default xinitrc, commented out the last few lines as suggested and added "exec cinnamon-session".  I trust that this was the 'right' thing to do:

.
.
.
if [ -d /etc/X11/xinit/xinitrc.d ] ; then
 for f in /etc/X11/xinit/xinitrc.d/?*.sh ; do
  [ -x "$f" ] && . "$f"
 done
 unset f
fi

#twm &
#xclock -geometry 50x50-1+1 &
#xterm -geometry 80x50+494+51 &
#xterm -geometry 80x20+494-0 &
#exec xterm -geometry 80x66+0+0 -name login
exec cinnamon-session

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#16 2016-03-14 12:41:15

Trilby
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Registered: 2011-11-29
Posts: 29,444
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Re: [Solved]Lots of authentication issues since pacman -Syu today

This is just another coincidence - or there is something important you are not telling us.  You were convinced that the other grub option solved the problem, but that was just a coincidence as you made other changes at the same time.  Now you are convinced it is the presence of the xinitrc, but this too is just a coincidence as you certainly made yet other changes at the same time.  I know this because if you are still using lightDM, lightDM does not read xinitrc, so the contents of xinitrc are either completely irrelevant, or you stopped using lightDM and failed to tell us.

Discontinuing use of lightDM could be a possible solution as DMs cause all sorts of problems.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#17 2016-03-14 15:34:25

PeterBell
Member
Registered: 2014-07-20
Posts: 39

Re: [Solved]Lots of authentication issues since pacman -Syu today

I have just wasted more than an hour constructing a reply to your post and found, when I came to submit it, that my login had expired, so have lost everything I typed. :'(

If I have the strength of will to retype it all (what I can remember) I may do so, but it's now 11.30 pm and I'm too tired to continue.

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