Just complete apt-get /update/upgrade and my system is bonked!

[Craig White]

Actually, the /usr/local/lib/libxml2.so.2.6.30 would not likely to have
been installed by apt/dpkg but likely by some tarball installation of
some package instead. The problem with tarball installations like this
is that the shell typically uses files in /usr/local before /usr and in
this case, it is a problem.

And the TLS errors would appear to be related to a VNC server starting
up...maybe normal, may not be normal...I don't know.

web servers aren't going to log in a ~/.xsession-errors anyway.

The openoffice.desktop errors are because launchers for a version that
is no longer installed are in some panel on your desktop. Remove
launchers, error goes away.

Craig

On Mon, 2009-06-22 at 19:06 -0700, Joseph Sinclair wrote:
> The missing file errors are leftovers.  Something in your system is still referencing the old OO.o version 2.4, and the new 3.0 version changed the filenames.  You can safely ignore that (or hunt down what's referencing the old files and fix it, if you're adventurous).
> libxml2 is used by a lot of software, don't remove it.
> Stick with apt and dpkg (APT is really a frontend for dpkg) as much as possible, it's easy to get borked when you go outside the fence...
> You can remove the renamed xml2lib.so.2.6.30.  It's borken, and is just wasting space now.
> The metacity missing file thing (/home/mark/.config/metacity/sessions/default0.ms: Failed to open file) is not uncommon, you simply don't have a saved session there.  Metacity will generally recover just fine and fix itself on that.
> AFAICT the authentication warnings are about SSL stuff (are you running a web server?).  I don't think those are a problem, but I'll defer to the more security-skilled on the list in this regard.
> 
> Mark Phillips wrote:
> > Joseph,
> > 
> > Thanks for the suggestions. When I reinstalled libxml2 there were no errors.
> > When I installed the librsvg2 apps, librsvg2-2 and librsvg2-common were
> > already the latest versions and librsvg2-bin was installed. After a reboot,
> > I still had the libxml2 errors in .xsession-errors.
> > 
> > I searched for libxml2.so, and the 2.6 version was still present. After some
> > googling on this error, It seems that vmware installed it (from tar.gz and
> > not apt), so it was not being maintained by apt. I removed vmware completely
> > but /usr/lib/libxml2.so.2.6.30 was still present. So, I renamed it
> > xml2lib.so.2.6.30 and reinstalled libxm2. After a reboot, my desktop icons
> > came back. Can I safely remove this file? How would I find out if another
> > program that I have not started still needs it? 99.99% of all my programs
> > are installed with apt; the vmware install was unusual.
> > 
> > I still have these errors in .xsession-errors:
> > /etc/gdm/Xsession: Beginning session setup...
> > SESSION_MANAGER=local/narwhale:@
> > /tmp/.ICE-unix/4441,unix/narwhale:/tmp/.ICE-unix/4441
> > Window manager warning: Failed to read saved session file
> > /home/mark/.config/metacity/sessions/default0.ms: Failed to open file
> > '/home/mark/.config/metacity/sessions/default0.ms': No such file or
> > directory
> > GNOME_KEYRING_SOCKET=/tmp/keyring-nSmW8a/socket
> > SSH_AUTH_SOCK=/tmp/keyring-nSmW8a/socket.ssh
> > 21/06/2009 08:22:45 AM Autoprobing TCP port
> > 21/06/2009 08:22:45 AM Autoprobing selected port 5900
> > 21/06/2009 08:22:45 AM Advertising security type: 'TLS' (18)
> > 21/06/2009 08:22:45 AM Advertising authentication type: 'No Authentication'
> > (1)
> > 21/06/2009 08:22:45 AM Advertising security type: 'No Authentication' (1)
> > 
> > ** (nautilus:4681): WARNING **: Unable to add monitor: Not supported
> > Unable to open desktop file
> > /usr/share/applications/openoffice.org2.4-writer.desktop for panel launcher:
> > No such file or directory
> > Unable to open desktop file
> > /usr/share/applications/openoffice.org2.4-calc.desktop for panel launcher:
> > No such file or directory
> > Unable to open desktop file
> > /usr/share/applications/openoffice.org2.4-base.desktop for panel launcher:
> > No such file or directory
> > ESC[31;01merror: No system tray detected on this system. Unable to start,
> > exiting. ESC[0m
> > Window manager warning: Invalid WM_TRANSIENT_FOR window 0x220000e specified
> > for 0x220000c (HPLIP Stat).
> > 
> > ESC[01mHP Linux Imaging and Printing System (ver. 1.7.4a)ESC[0m
> > ESC[01mSystem Tray Status Service ver. 2.0ESC[0m
> > 
> > Copyright (c) 2001-9 Hewlett-Packard Development Company, LP
> > This software comes with ABSOLUTELY NO WARRANTY.
> > This is free software, and you are welcome to distribute it
> > under certain conditions. See COPYING file for more details.
> > 
> > Should I be concerned about the warnings and missing authentication? How do
> > I fix them?
> > 
> > Thanks for all your help!!!!
> > 
> > Mark
> > 
> > On Sat, Jun 20, 2009 at 11:40 PM, Joseph Sinclair <plug-discussion at stcaz.net
> >> wrote:
> > 
> >> You have a couple problems that I can see from this:
> >> 1) libxml is horked.  This is pretty bad (because of all the xml in the
> >> Gnome configs), but can be fixed
> >> 2) Nautilus is failing to start due to missing core library dependencies,
> >> this is what's causing your no-desktop issues.
> >>
> >> try the following:
> >> sudo apt-get install --reinstall libxml2
> >> sudo apt-get install librsvg2-2 librsvg2-common librsvg2-bin
> >>
> >> that may get you to a more stable state.
> >>
> >> It's possible that you're just a bit too far out in front of the devs with
> >> Squeeze, so you may have to wait a bit for them to get librsvg-2 properly
> >> packaged for you before Gnome will work again...
> >>
> >> Mark Phillips wrote:
> >>> Joseph,
> >>>
> >>> This is in .xsession-errors:
> >>> /etc/gdm/Xsession: Beginning session setup...
> >>> SESSION_MANAGER=local/narwhale:@
> >>> /tmp/.ICE-unix/4168,unix/narwhale:/tmp/.ICE-unix/4168
> >>> 1245556817.745420 Session manager: disconnected...
> >>> Warning: program compiled against libxml 207 using older 206
> >>> Warning: program compiled against libxml 207 using older 206
> >>> Warning: program compiled against libxml 207 using older 206
> >>> Window manager warning: Failed to read saved session file
> >>> /home/mark/.config/metacity/sessions/default0.ms: Failed to open file
> >>> '/home/mark/.config/metacity/sessions/default0.ms': No such file or
> >>> directory
> >>> Warning: program compiled against libxml 207 using older 206
> >>> Warning: program compiled against libxml 207 using older 206
> >>> Warning: program compiled against libxml 207 using older 206
> >>> Warning: program compiled against libxml 207 using older 206
> >>> GNOME_KEYRING_SOCKET=/tmp/keyring-u7nyMw/socket
> >>> SSH_AUTH_SOCK=/tmp/keyring-u7nyMw/socket.ssh
> >>> Warning: program compiled against libxml 207 using older 206
> >>> 20/06/2009 09:00:31 PM Autoprobing TCP port
> >>> 20/06/2009 09:00:31 PM Autoprobing selected port 5900
> >>> 20/06/2009 09:00:31 PM Advertising security type: 'TLS' (18)
> >>> 20/06/2009 09:00:31 PM Advertising authentication type: 'No
> >> Authentication'
> >>> (1)
> >>> 20/06/2009 09:00:31 PM Advertising security type: 'No Authentication' (1)
> >>>
> >>> ** (nautilus:4409): WARNING **: Unable to add monitor: Not supported
> >>> nautilus: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined symbol:
> >>> xmlNewEntity
> >>>
> >>> (nautilus:4417): Unique-DBus-WARNING **: Error while sending message:
> >>> Message did not receive a reply (timeout by message bus)
> >>> Unable to open desktop file
> >>> /usr/share/applications/openoffice.org2.4-writer.desktop for panel
> >> launcher:
> >>> No such file or directory
> >>> Unable to open desktop file
> >>> /usr/share/applications/openoffice.org2.4-calc.desktop for panel
> >> launcher:
> >>> No such file or directory
> >>> Unable to open desktop file
> >>> /usr/share/applications/openoffice.org2.4-base.desktop for panel
> >> launcher:
> >>> No such file or directory
> >>> Warning: program compiled against libxml 207 using older 206
> >>> epiphany-browser: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined
> >>> symbol: xmlNewEntity
> >>> Warning: program compiled against libxml 207 using older 206
> >>> epiphany-browser: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined
> >>> symbol: xmlNewEntity
> >>> Warning: program compiled against libxml 207 using older 206
> >>> Warning: program compiled against libxml 207 using older 206
> >>> epiphany-browser: symbol lookup error: /usr/lib/librsvg-2.so.2: undefined
> >>> symbol: xmlNewEntity
> >>> nsHeaderInfo: registerSelf called!
> >>> nsHeaderInfo: registerSelf called!
> >>>
> >>> compiz was not installed for some reason, so I tried installing it, but
> >> no
> >>> change.
> >>> It appears that I have two versions of libxml2 installed -
> >>> /usr/lib/libxml2.so.2.7.3
> >>> /usr/local/lib/libxml2.so.2.6.30
> >>> but dpkg says I only have one:
> >>> narwhale:/home/mark# dpkg -l libxml2*
> >>> Desired=Unknown/Install/Remove/Purge/Hold
> >>> |
> >>>
> >> Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend
> >>> |/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err:
> >>> uppercase=bad)
> >>> ||/ Name Version Description
> >>>
> >> +++-=========================-=========================-==================================================================
> >>> ii libxml2 2.7.3.dfsg-1 GNOME XML library
> >>> un libxml2-dev <none> (no description available)
> >>> un libxml2-doc <none> (no description available)
> >>> un libxml2-headers <none> (no description available)
> >>> un libxml2-python2.3 <none> (no description available)
> >>> ii libxml2-utils 2.7.3.dfsg-1 XML utilities
> >>> narwhale:/home/mark#
> >>>
> >>> I remember several of those warning about libxml during apt-get upgrade.
> >> I
> >>> don't know if this is the problem, but one of the errors in
> >> .xsession-errors
> >>> mentions an unknown xml entry.
> >>> I don't know how to "blow away" my gconf or gnome configuration as
> >> suggested
> >>> by James, nor do I understand if that will help.
> >>>
> >>> Any further suggestions would be greatly appreciated!
> >>>
> >>> Mark
> >>>
> >>>
> >>> On Sat, Jun 20, 2009 at 7:21 PM, Joseph Sinclair
> >>> <plug-discussion at stcaz.net>wrote:
> >>>
> >>>> From the sound of it Nautilus is not starting or failing on startup.
> >>>> Have you looked at .xsession-errors?  There may be something there about
> >> a
> >>>> dbus failure.
> >>>> Try (from a command-line if you can get a terminal started) running
> >>>> nautilus directly, if that "fixes" the problem, then you know for
> >> certain
> >>>> what's failing (you might also get debug output that can help tell you
> >> why).
> >>>> If you can't start Nautilus, try disabling compiz, sometimes that causes
> >>>> problems during upgrades.
> >>>> I had a similar problem in a stable release, and I had some luck with
> >> (via
> >>>> command-line) disabling compiz and dropping back to a simpler graphics
> >>>> driver (kernel drivers first, VESA if those fail).  You might have some
> >> luck
> >>>> trying that.
> >>>> If all else fails, you might need to blow away your gnome configuration
> >>>> files (back them up first!) as suggested by James.
> >>>>
> >>>>
> >>>> Mark Phillips wrote:
> >>>>> I am running Debian testing on my laptop. Just completed a routine
> >>>> apt-get
> >>>>> update apt-get upgrade, and now all my desktop icons are gone and every
> >>>> time
> >>>>> I access the menus (Applications, Places, System) the upper and lower
> >>>> menu
> >>>>> bars disappear and then come back. I am writing this email in a browser
> >>>>> window, so once an application is launched it seems to work OK.
> >>>>>
> >>>>> I have no idea where to start debugging this problem. Any suggestions
> >> are
> >>>>> welcome!
> >>>>>
> >>>>> Mark
> >>>>>
> >>>>> P.S. I am running gnome, not KDE. Also, I cannot right click on the
> >>>> desktop
> >>>>> - nothing happens.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
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