Problem when updating modules for 12.04.5

I am no expert in MySQL, but have some knowledge about package management.
It seems that for whatever reason the postinst script of the mysql-server-5.5 package runs into an error.

Please execute the terminal commands

sudo bash -x /var/lib/dpkg/info/mysql-server-5.5.postinst configure
echo $?

and paste the last 20 lines of the output into this question document. (In case that passwords are shown in that output please replace them by XXXs.)

>sudo bash -x /var/lib/dpkg/info/mysql-server-5.5.postinst configure
+ . /usr/share/debconf/confmodule
++ '[' '!' '' ']'
++ PERL_DL_NONLAZY=1
++ export PERL_DL_NONLAZY
++ '[' '' ']'
++ exec /usr/share/debconf/frontend /var/lib/dpkg/info/mysql-server-5.5.postinst configure
Rather than invoking init scripts through /etc/init.d, use the service(8)
utility, e.g. service mysql stop
initctl: Unknown job: mysql

Since the script you are attempting to invoke has been converted to an
Upstart job, you may also use the stop(8) utility, e.g. stop MySQL

(Then it just hangs)

Also the above command first gives me a window to change my password for MySQL. If I leave it back, the password remains the same. Then goes back to the terminal with the above output and just hangs.
(Control Z)
>kill job 1
>echo $?
130

There seems to be a problem with initctl - init daemon control tool

What is the output of

initctl list
sudo initctl reload-configuration
initctl list
initctl status mysqld

>initctl list
mountall-net stop/waiting
passwd stop/waiting
rc stop/waiting
rsyslog start/running, process 728
screen-cleanup stop/waiting
tty4 start/running, process 1155
udev start/running, process 375
upstart-udev-bridge start/running, process 365
ureadahead-other stop/waiting
vmware-tools stop/waiting
whoopsie start/running, process 1406
apport start/running
console-setup stop/waiting
hwclock-save stop/waiting
irqbalance stop/waiting
plymouth-log stop/waiting
tty5 start/running, process 1161
failsafe stop/waiting
atd start/running, process 1181
dbus start/running, process 637
mounted-var stop/waiting
plymouth stop/waiting
resolvconf start/running
ssh start/running, process 821
udev-fallback-graphics stop/waiting
control-alt-delete stop/waiting
hwclock stop/waiting
mounted-proc stop/waiting
module-init-tools stop/waiting
setvtrgb stop/waiting
shutdown stop/waiting
cron start/running, process 1180
mountall stop/waiting
mounted-debugfs stop/waiting
console stop/waiting
mounted-run stop/waiting
acpid start/running, process 1178
plymouth-stop stop/waiting
rcS stop/waiting
ufw start/running
wait-for-state stop/waiting
flush-early-job-log stop/waiting
friendly-recovery stop/waiting
rc-sysinit stop/waiting
upstart-socket-bridge start/running, process 1127
tty2 start/running, process 1172
udevtrigger stop/waiting
container-detect stop/waiting
mounted-dev stop/waiting
tty3 start/running, process 1173
udev-finish stop/waiting
hostname stop/waiting
mountall-reboot stop/waiting
mountall-shell stop/waiting
mounted-tmp stop/waiting
network-interface (lo) start/running
network-interface (eth0) start/running
plymouth-ready stop/waiting
plymouth-splash stop/waiting
plymouth-upstart-bridge stop/waiting
tty1 start/running, process 3023
udevmonitor stop/waiting
dmesg stop/waiting
network-interface-security (network-interface/eth0) start/running
network-interface-security (network-interface/lo) start/running
network-interface-security (networking) start/running
networking stop/waiting
procps stop/waiting
tty6 start/running, process 1175
network-interface-container stop/waiting
ureadahead stop/waiting
vsftpd start/running, process 911

>initctl reload-configuration
>(nothing)

>initctl list
rsyslog start/running, process 728
tty4 start/running, process 1155
udev start/running, process 375
upstart-udev-bridge start/running, process 365
whoopsie start/running, process 1406
mountall-net stop/waiting
passwd stop/waiting
rc stop/waiting
screen-cleanup stop/waiting
ureadahead-other stop/waiting
vmware-tools stop/waiting
apport start/running
tty5 start/running, process 1161
console-setup stop/waiting
hwclock-save stop/waiting
irqbalance stop/waiting
plymouth-log stop/waiting
failsafe stop/waiting
atd start/running, process 1181
dbus start/running, process 637
resolvconf start/running
ssh start/running, process 821
mounted-var stop/waiting
plymouth stop/waiting
udev-fallback-graphics stop/waiting
control-alt-delete stop/waiting
hwclock stop/waiting
mounted-proc stop/waiting
module-init-tools stop/waiting
setvtrgb stop/waiting
shutdown stop/waiting
cron start/running, process 1180
mountall stop/waiting
mounted-debugfs stop/waiting
console stop/waiting
mounted-run stop/waiting
acpid start/running, process 1178
ufw start/running
plymouth-stop stop/waiting
rcS stop/waiting
wait-for-state stop/waiting
flush-early-job-log stop/waiting
friendly-recovery stop/waiting
rc-sysinit stop/waiting
upstart-socket-bridge start/running, process 1127
tty2 start/running, process 1172
udevtrigger stop/waiting
tty3 start/running, process 1173
container-detect stop/waiting
mounted-dev stop/waiting
udev-finish stop/waiting
hostname stop/waiting
mountall-reboot stop/waiting
network-interface (lo) start/running
network-interface (eth0) start/running
tty1 start/running, process 3023
mountall-shell stop/waiting
mounted-tmp stop/waiting
plymouth-ready stop/waiting
plymouth-splash stop/waiting
plymouth-upstart-bridge stop/waiting
udevmonitor stop/waiting
network-interface-security (network-interface/eth0) start/running
network-interface-security (network-interface/lo) start/running
network-interface-security (networking) start/running
tty6 start/running, process 1175
dmesg stop/waiting
networking stop/waiting
procps stop/waiting
vsftpd start/running, process 911
network-interface-container stop/waiting
ureadahead stop/waiting

>initctl status mysqld
initctl: Unknown job: mysqld

Do you think this is a permission issue with MySQL or possibly does MySQL need to be stopped before updating?

it seems to me that initctl has - for whatever reason - totally lost the information about mysqld, it cannot start or stop it.

What is the output of

ls -l /etc/init/mysql*

>ls -l /etc/init/mysql*
-rw-r--r-- 1 root root 1770 Jan 21 2014 /etc/init/mysql.conf_old_v5.5

Try

sudo dpkg --audit
sudo dpkg -i /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb

and report the output.

>sudo dpkg --audit
The following packages have been unpacked but not yet configured.
They must be configured using dpkg --configure or the configure
menu option in dselect for them to work:
 apt-transport-https https download transport for APT
 libapt-inst1.4 deb package format runtime library
 apt-utils package managment related utility programs
 mysql-server MySQL database server (metapackage depending on the lates

The following packages are only half configured, probably due to problems
configuring them the first time. The configuration should be retried using
dpkg --configure <package> or the configure menu option in dselect:
 mysql-server-5.5 MySQL database server binaries and system database setup

>sudo dpkg -i /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb
dpkg: error processing /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb (--install):
 cannot access archive: No such file or directory
Errors were encountered while processing:
 /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb

ok, it seems that I assumed something that is not the case.

Try

sudo apt-get --download-only install mysql-server-5.5
ls -l /var/cache/apt/archives/mysql-server-*
sudo dpkg -i /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb

and report the output.

>sudo apt-get --download-only install mysql-server-5.5
Reading package lists... Done
Building dependency tree
Reading state information... Done
mysql-server-5.5 is already the newest version.
The following packages were automatically installed and are no longer required:
  linux-headers-3.2.0-70-generic linux-image-3.2.0-76-generic linux-headers-3.2.0-70
  linux-headers-3.2.0-72 linux-headers-3.2.0-74 linux-headers-3.2.0-76 linux-headers-3.2.0-77
  linux-headers-3.2.0-76-generic linux-image-3.2.0-74-generic linux-image-3.2.0-77-generic
  linux-headers-3.2.0-74-generic linux-image-3.2.0-72-generic linux-headers-3.2.0-77-generic
  linux-headers-3.2.0-72-generic linux-image-3.2.0-70-generic
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
5 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue [Y/n]? y
Download complete and in download only mode

>ls -l /var/cache/apt/archives/mysql-server-*
ls: cannot access /var/cache/apt/archives/mysql-server-*: No such file or directory

>sudo dpkg -i /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb

dpkg: error processing /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb (--install):
 cannot access archive: No such file or directory
Errors were encountered while processing:
 /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb

I also am listing the contents of the /var/cache/apt/archives directory to see if there is a permission issue...?

> ls -als /var/cache/apt/archives
total 2304
   4 drwxr-xr-x 3 root root 4096 Apr 23 09:26 .
   4 drwxr-xr-x 3 root root 4096 Apr 24 06:35 ..
1072 -rw-r--r-- 1 root root 1096990 Mar 11 19:24 apt_0.8.16~exp12ubuntu10.23_amd64.deb
  16 -rw-r--r-- 1 root root 16336 Mar 11 19:24 apt-transport-https_0.8.16~exp12ubuntu10.23_amd64.deb
 188 -rw-r--r-- 1 root root 188932 Mar 11 19:24 apt-utils_0.8.16~exp12ubuntu10.23_amd64.deb
 100 -rw-r--r-- 1 root root 102050 Mar 11 19:24 libapt-inst1.4_0.8.16~exp12ubuntu10.23_amd64.deb
 916 -rw-r--r-- 1 root root 935282 Mar 11 19:24 libapt-pkg4.12_0.8.16~exp12ubuntu10.23_amd64.deb
   0 -rw-r----- 1 root root 0 Feb 7 2014 lock
   4 drwxr-xr-x 2 root root 4096 Apr 23 09:26 partial

There's nothing in the "lock" file.

I expected that all downloaded packages are stored in the /var/cache/apt/archives directory. This seems not to be the case for your system. (Maybe there is a job running to empty that directory periodically, or your apt/dpkg configuration specifies that the files are stored elsewhere.)

Ok, let's try it differently:

open a terminal and issue the commands

cd
uname -a
wget -c http://security.ubuntu.com/ubuntu/pool/main/m/mysql-5.5/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb
sudo dpkg -i ~/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb

and report the outcome.

On another parallel machine that is running the same system, I have the following files in that archives directory. Are these the ones that you are looking for? If I copy them to the problematic Linux box, will the apt-get upgrade work?
> ls -l /var/cache/apt/archives/mysql-server-*
-rw-r--r-- 1 root root 8849954 Apr 21 10:03 /var/cache/apt/archives/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb
-rw-r--r-- 1 root root 6097130 Apr 21 10:03 /var/cache/apt/archives/mysql-server-core-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb

>uname -a
Linux oak-lso-momrp 3.2.0-80-generic #116-Ubuntu SMP Mon Mar 23 17:11:03 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

>wget -c http://security.ubuntu.com/ubuntu/pool/main/m/mysql-5.5/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb
--2015-04-26 14:19:50-- http://security.ubuntu.com/ubuntu/pool/main/m/mysql-5.5/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.91.14, 91.189.92.200, 91.189.88.149, ...
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.91.14|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 8849954 (8.4M) [application/x-debian-package]
Saving to: `mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb'

100%[==============================================================>] 8,849,954 3.84M/s in 2.2s

2015-04-26 14:19:52 (3.84 MB/s) - `mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb' saved [8849954/8849954]

>dpkg -i ~/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb
(Reading database ... 249714 files and directories currently installed.)
Preparing to replace mysql-server-5.5 5.5.43-0ubuntu0.12.04.1 (using .../mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb) ...
initctl: Unknown job: mysql
Unpacking replacement mysql-server-5.5 ...
initctl: Unknown job: mysql
Setting up mysql-server-5.5 (5.5.43-0ubuntu0.12.04.1) ...
initctl: Unknown job: mysql

>root@oak-lso-momrp:~# wget -c http://security.ubuntu.com/ubuntu/pool/main/m/mysql-5.5/mysql-server-core-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb
--2015-04-26 14:23:33-- http://security.ubuntu.com/ubuntu/pool/main/m/mysql-5.5/mysql-server-core-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.91.14, 91.189.91.23, 91.189.91.13, ...
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.91.14|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6097130 (5.8M) [application/x-debian-package]
Saving to: `mysql-server-core-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb'

100%[==============================================================>] 6,097,130 4.70M/s in 1.2s

2015-04-26 14:23:35 (4.70 MB/s) - `mysql-server-core-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb' saved [6097130/6097130]

>dpkg -i ~/mysql-server-core-5.5_5.5.43-0ubuntu0.12.04.1_*.deb
(Reading database ... 249714 files and directories currently installed.)
Preparing to replace mysql-server-core-5.5 5.5.43-0ubuntu0.12.04.1 (using .../mysql-server-core-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb) ...
Unpacking replacement mysql-server-core-5.5 ...
Setting up mysql-server-core-5.5 (5.5.43-0ubuntu0.12.04.1) ...
Processing triggers for man-db ...
>

(retry)
>dpkg -i ~/mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_*.deb (Reading database ... 249714 files and directories currently installed.)
Preparing to replace mysql-server-5.5 5.5.43-0ubuntu0.12.04.1 (using .../mysql-server-5.5_5.5.43-0ubuntu0.12.04.1_amd64.deb) ...
initctl: Unknown job: mysql
Unpacking replacement mysql-server-5.5 ...
initctl: Unknown job: mysql
Setting up mysql-server-5.5 (5.5.43-0ubuntu0.12.04.1) ...
initctl: Unknown job: mysql

> ps aux
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
root 1 0.7 0.0 24332 2240 ? Ss 14:38 0:01 /sbin/init
root 2 0.0 0.0 0 0 ? S 14:38 0:00 [kthreadd]
root 3 0.1 0.0 0 0 ? S 14:38 0:00 [ksoftirqd/0]
root 4 0.0 0.0 0 0 ? S 14:38 0:00 [kworker/0:0]
root 5 0.1 0.0 0 0 ? S 14:38 0:00 [kworker/u:0]
root 6 0.0 0.0 0 0 ? S 14:38 0:00 [migration/0]
root 7 0.0 0.0 0 0 ? S 14:38 0:00 [watchdog/0]
root 8 0.0 0.0 0 0 ? S< 14:38 0:00 [cpuset]
root 9 0.0 0.0 0 0 ? S< 14:38 0:00 [khelper]
root 10 0.0 0.0 0 0 ? S 14:38 0:00 [kdevtmpfs]
root 11 0.0 0.0 0 0 ? S< 14:38 0:00 [netns]
root 12 0.0 0.0 0 0 ? S 14:38 0:00 [sync_supers]
root 13 0.0 0.0 0 0 ? S 14:38 0:00 [bdi-default]
root 14 0.0 0.0 0 0 ? S< 14:38 0:00 [kintegrityd]
root 15 0.0 0.0 0 0 ? S< 14:38 0:00 [kblockd]
root 16 0.0 0.0 0 0 ? S< 14:38 0:00 [ata_sff]
root 17 0.0 0.0 0 0 ? S 14:38 0:00 [khubd]
root 18 0.0 0.0 0 0 ? S< 14:38 0:00 [md]
root 19 0.0 0.0 0 0 ? S 14:38 0:00 [kworker/u:1]
root 21 0.0 0.0 0 0 ? S 14:38 0:00 [khungtaskd]
root 22 0.0 0.0 0 0 ? S 14:38 0:00 [kswapd0]
root 23 0.0 0.0 0 0 ? SN 14:38 0:00 [ksmd]
root 24 0.0 0.0 0 0 ? SN 14:38 0:00 [khugepaged]
root 25 0.0 0.0 0 0 ? S 14:38 0:00 [fsnotify_mark]
root 26 0.0 0.0 0 0 ? S 14:38 0:00 [ecryptfs-kthrea]
root 27 0.0 0.0 0 0 ? S< 14:38 0:00 [crypto]
root 35 0.0 0.0 0 0 ? S< 14:38 0:00 [kthrotld]
root 36 0.0 0.0 0 0 ? S 14:38 0:00 [kworker/0:1]
root 37 0.0 0.0 0 0 ? S 14:38 0:00 [scsi_eh_0]
root 38 0.0 0.0 0 0 ? S 14:38 0:00 [scsi_eh_1]
root 39 0.0 0.0 0 0 ? S 14:38 0:00 [kworker/u:2]
root 40 0.0 0.0 0 0 ? S 14:38 0:00 [kworker/u:3]
root 59 0.0 0.0 0 0 ? S< 14:38 0:00 [devfreq_wq]
root 60 0.0 0.0 0 0 ? R 14:38 0:00 [kworker/0:2]
root 179 0.0 0.0 0 0 ? S< 14:38 0:00 [mpt_poll_0]
root 224 0.0 0.0 0 0 ? S< 14:38 0:00 [mpt/0]
root 278 0.0 0.0 0 0 ? S 14:38 0:00 [scsi_eh_2]
root 292 0.0 0.0 0 0 ? S< 14:38 0:00 [kdmflush]
root 302 0.0 0.0 0 0 ? S< 14:38 0:00 [kdmflush]
root 315 0.0 0.0 0 0 ? S 14:38 0:00 [jbd2/dm-0-8]
root 316 0.0 0.0 0 0 ? S< 14:38 0:00 [ext4-dio-unwrit]
root 427 0.0 0.0 17360 900 ? S 14:38 0:00 upstart-udev-bridge --daemon
root 432 0.0 0.0 21988 1800 ? Ss 14:38 0:00 /sbin/udevd --daemon
root 713 0.0 0.0 0 0 ? S< 14:38 0:00 [kpsmoused]
102 716 0.0 0.0 23924 992 ? Ss 14:38 0:00 dbus-daemon --system --fork --activatio
root 750 0.0 0.0 21984 1316 ? S 14:38 0:00 /sbin/udevd --daemon
root 751 0.0 0.0 21968 1340 ? S 14:38 0:00 /sbin/udevd --daemon
root 772 0.0 0.0 0 0 ? S< 14:38 0:00 [ttm_swap]
syslog 800 0.0 0.0 249464 1492 ? Sl 14:38 0:00 rsyslogd -c5
root 888 0.0 0.0 50032 2912 ? Ss 14:38 0:00 /usr/sbin/sshd -D
root 919 0.0 0.0 23432 1916 ? Ss 14:38 0:00 /usr/sbin/vsftpd
root 1117 0.0 0.0 15184 388 ? S 14:38 0:00 upstart-socket-bridge --daemon
root 1203 0.0 0.0 15780 964 tty4 Ss+ 14:38 0:00 /sbin/getty -8 38400 tty4
root 1209 0.0 0.0 15780 972 tty5 Ss+ 14:38 0:00 /sbin/getty -8 38400 tty5
root 1213 0.0 0.0 15780 972 tty2 Ss+ 14:38 0:00 /sbin/getty -8 38400 tty2
root 1214 0.0 0.0 15780 968 tty3 Ss+ 14:38 0:00 /sbin/getty -8 38400 tty3
root 1216 0.0 0.0 15780 968 tty6 Ss+ 14:38 0:00 /sbin/getty -8 38400 tty6
root 1220 0.0 0.0 19108 1008 ? Ss 14:38 0:00 cron
daemon 1221 0.0 0.0 16904 372 ? Ss 14:38 0:00 atd
root 1233 0.0 0.0 4324 684 ? Ss 14:38 0:00 acpid -c /etc/acpi/events -s /var/run/a
whoopsie 1543 0.0 0.1 187660 4088 ? Ssl 14:38 0:00 whoopsie
106 1544 0.0 0.0 47472 1016 ? Ss 14:38 0:00 /usr/sbin/exim4 -bd -q30m
root 1747 0.0 0.0 4396 736 ? S 14:38 0:00 /bin/sh /opt/mysql/server-5.6/bin/mysql
root 2309 0.0 0.0 0 0 ? S 14:38 0:00 [flush-8:0]
root 2316 0.0 0.0 0 0 ? S 14:38 0:00 [flush-252:0]
mysql 2751 0.4 18.0 3940816 729884 ? Sl 14:38 0:00 /opt/mysql/server-5.6/bin/mysqld --base
nagios 2923 0.0 0.0 25424 1160 ? Ss 14:38 0:00 /usr/sbin/nrpe -c /etc/nagios/nrpe.cfg
root 2955 0.0 0.3 48124 13236 ? Ss 14:38 0:00 /usr/bin/perl -w /usr/sbin/psad
root 2961 0.0 0.0 4300 304 ? Ss 14:38 0:00 /usr/sbin/psadwatchd -c /etc/psad/psad.
root 3004 0.0 0.2 193528 8528 ? Ss 14:38 0:00 /usr/sbin/apache2 -k start
www-data 3023 0.0 0.1 193552 5176 ? S 14:38 0:00 /usr/sbin/apache2 -k start
www-data 3024 0.0 0.1 193552 5176 ? S 14:38 0:00 /usr/sbin/apache2 -k start
www-data 3025 0.0 0.1 193552 5176 ? S 14:38 0:00 /usr/sbin/apache2 -k start
www-data 3026 0.0 0.1 193552 5176 ? S 14:38 0:00 /usr/sbin/apache2 -k start
www-data 3027 0.0 0.1 193552 5176 ? S 14:38 0:00 /usr/sbin/apache2 -k start
root 3032 0.0 0.1 195576 7328 ? Sl 14:38 0:00 /usr/bin/python /usr/bin/fail2ban-serve
root 3034 0.0 0.0 22392 1440 ? S 14:38 0:00 /usr/lib/gamin/gam_server
root 3064 0.0 0.0 15780 968 tty1 Ss+ 14:38 0:00 /sbin/getty -8 38400 tty1
root 4166 0.0 0.0 47468 2716 ? Ss 14:40 0:00 /usr/sbin/exim4 -Mc 1YmRTU-00012q-T6
106 4256 0.0 0.0 47760 1564 ? S 14:40 0:00 /usr/sbin/exim4 -Mc 1YmRTU-00012q-T6
root 4370 0.0 0.0 4396 608 ? S 14:40 0:00 /bin/sh /etc/init.d/ondemand background
root 4372 0.0 0.0 4304 348 ? S 14:40 0:00 sleep 60
root 4857 0.0 0.0 73436 3580 ? Ss 14:40 0:00 sshd: gillh [priv]
root 4876 0.0 0.0 73436 3552 ? Ss 14:40 0:00 sshd: gillh [priv]
gillh 5006 0.0 0.0 73436 1936 ? S 14:40 0:00 sshd: gillh@pts/0
gillh 5024 0.6 0.1 26452 7636 pts/0 Ss 14:40 0:00 -bash
gillh 5162 0.0 0.0 73436 1676 ? S 14:40 0:00 sshd: gillh@notty
gillh 5200 0.0 0.0 12772 740 ? Ss 14:40 0:00 /usr/lib/openssh/sftp-server
root 5260 0.0 0.0 39160 1824 pts/0 S 14:40 0:00 sudo -i
root 5263 0.6 0.1 23020 4304 pts/0 S 14:40 0:00 -bash

I'm not sure what I did: here were my steps:
>apt-get autoremove
(deleted files)
>apt-get -f install
(worked this time; no MySQL error not found)
>apt-get update
(worked)
>apt-get upgradeReading package lists... Done
Building dependency tree
Reading state information... Done
The following packages have been kept back:
  landscape-common
0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.

Question 1: Am I updated now?
Question 2: What is the difference between apt-get upgrade and apt-get install? They give the same output.

Question 3: Which "1" is not upgraded? I get the same message on my other box that is running fine.

Thank you Manfred. I appreciate your help tremendously. I have learned a lot as well.

I have another problem on another ubuntu machine. May I ask it here, or should start a new thread?

If you have another question/problem, please start a new thread.
Each question document should be focusing on one single problem.