My computer just recently came up with an update to the mesa GL program. This was not odd except that the button to select it was grayed out, which did not allow me to select it for upgrade. I then went to the terminal WINDOW to install it manually. (possibly my first mistake) This is the output it gave me:
$ sudo apt-get install libgl1-mesa-swx11
[sudo] password:
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer REQUIRED:
  browser-plugin-gnash menu-xdg libkactivities5 ekiga gnuchess-book
  gnome-games-extra-data gtali glchess libkimproxy4 libclutter-gst-1.0-0
  gnome-video-effects libkdeclarative5 libdiscid0 gnome-games cheese gdebi
  quadrapassel gnobots2 libfolks-eds25 liferea-data cheese-common libcheese1
  gdebi-core python-lxml libclutter-gtk-1.0-0 kdelibs5-dbg gnibbles
  gedit-plugins libpt2.10.2 libqt4-dbg libboost-date-time1.46.1 gnotski
  gnome-backgrounds libkrossui4 libspandsp2 libcluttergesture-0.0.2-0
  libknewstuff2-4 iagno glines gnome-icon-theme-extras gir1.2-gucharmap-2.90
  libmagick++3 libmx-1.0-2 kdebase-runtime-dbg python-uniconvertor
  libopal3.10.2 liferea gnash gnotravex libcheese-gtk20 gnect python-evolution
  gnome-contacts libkunitconversion4 kde-runtime-dbg hamster-applet gnuchess
  gnash-common perlmagick libclutter-imcontext-0.1-0 inkscape dconf-tools
  libkutils4 sound-juicer libmusicbrainz3-6
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
  fglrx fglrx-amdcccle fglrx-dev
The following packages will be upgraded:
  libgl1-mesa-swx11
1 upgraded, 0 newly installed, 3 to remove and 4 not upgraded.
Need to get 910 kB of archives.
After this operation, 81.9 MB disk space will be freed.
Do you want to continue [Y/n]? y
Get:1 http://us.archive.ubuntu.com/ubuntu/ oneiric/main libgl1-mesa-swx11 i386 7.11-0ubuntu3 [910 kB]
Fetched 910 kB in 8s (109 kB/s)                                               
(Reading database ... 231471 files and directories currently installed.)
Removing fglrx-dev ...
Removing fglrx-amdcccle ...
Removing fglrx ...
Removing all DKMS Modules
Done.
update-alternatives: using /usr/lib/pxpress/ld.so.conf to provide /etc/ld.so.conf.d/i386-linux-gnu_GL.conf (i386-linux-gnu_gl_conf) in auto mode.
update-alternatives: warning: skip creation of /usr/bin/amdcccle because associated file /usr/lib/fglrx/bin/amdcccle (of link group i386-linux-gnu_gl_conf) doesn't exist.
update-alternatives: warning: skip creation of /usr/share/applications/ubuntu-amdcccle.desktop because associated file /usr/share/fglrx/amdcccle.desktop (of link group i386-linux-gnu_gl_conf) doesn't exist.
update-alternatives: warning: skip creation of /usr/share/applications/ubuntu-amdccclesu.desktop because associated file /usr/share/fglrx/amdccclesu.desktop (of link group i386-linux-gnu_gl_conf) doesn't exist.
update-alternatives: warning: skip creation of /usr/bin/amdupdaterandrconfig because associated file /usr/lib/fglrx/bin/amdupdaterandrconfig (of link group i386-linux-gnu_gl_conf) doesn't exist.
update-alternatives: warning: skip creation of /usr/bin/amdxdg-su because associated file /usr/lib/fglrx/bin/amdxdg-su (of link group i386-linux-gnu_gl_conf) doesn't exist.
update-alternatives: warning: skip creation of /usr/lib32/libaticalcl.so because associated file /usr/lib32/fglrx/libaticalcl.so (of link group i386-linux-gnu_gl_conf) doesn't exist.
update-alternatives: warning: skip creation of /usr/lib32/libaticalrt.so because associated file /usr/lib32/fglrx/libaticalrt.so (of link group i386-linux-gnu_gl_conf) doesn't exist.
update-alternatives: warning: not replacing /usr/lib/i386-linux-gnu/xorg/extra-modules with a link.
update-alternatives: using /usr/lib/pxpress/alt_ld.so.conf to provide /etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf (x86_64-linux-gnu_gl_conf) in auto mode.
update-initramfs: deferring update (trigger activated)
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf.index...
Processing triggers for gnome-menus ...
Processing triggers for ureadahead ...
Processing triggers for initramfs-tools ...
update-initramfs: Generating /boot/initrd.img-3.0.0-15-generic
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
(Reading database ... 231239 files and directories currently installed.)
Preparing to replace libgl1-mesa-swx11 7.10.2-0ubuntu2.1 (using .../libgl1-mesa-swx11_7.11-0ubuntu3_i386.deb) ...
Unpacking replacement libgl1-mesa-swx11 ...
Setting up libgl1-mesa-swx11 (7.11-0ubuntu3) ...
update-alternatives: using /usr/lib/i386-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/i386-linux-gnu_GL.conf (i386-linux-gnu_gl_conf) in auto mode.
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
$


I wouldn't be so worried except that I just recently tweaked Ubuntu 11.10 in certain ways that had possible errors in them such as rendering the OS incapable to booting. The instructions I got off a page I trust but I fear that RUNNING this update somehow might have done irreparable damage to my OS. I still would not be worried except that one, the "update" got rid of more programs than it installed/upgraded and TWO, created a new boot image on a seemingly inconsequential graphics package.


Computer:
Dell Dimension 4550 running Ubuntu 11.10
748 MB of RAM
Pentium IV Processor at 2.53 GHZ
Rage 128 Pro Ultra 32 MB graphics card
Maxtor Hard Drive


If there's anything else you need, please let me know! Thank you!

initrd contains insmod (amongst other things), for loading kernel modules.  My guess is that the upgrade to Mesa requires a slight change to this program.  If you're concerned though, your best bet is to take an image of your system using CloneZilla, immediately before the upgrade.  That way, you can roll back if anything goes wrong.Thank you! Got the issue fixed (though it really wasn't an issue) I rebooted my computer and all was okay. Thanks again!No problem, although I don't think I did anything!  Glad it's SORTED.