I am using Ubuntu 12.04.2 LTS (“precise”). I am trying to upgrade all packages using kernel via apt-get upgrade method. But, I am getting the following message:

apt-get upgrade
Reading package lists… Done
Building dependency tree
Reading state information… Done
The following packages have been kept back:
linux-headers-virtual linux-image-virtual mysql-client-5.5 mysql-server-5.5
mysql-server-core-5.5
The following packages will be upgraded:
base-files dosfstools linux-libc-dev linux-libc-dev:i386
4 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Need to get 1,847 kB of archives.
After this operation, 2,048 B of additional disk space will be used.
Do you want to continue [Y/n]?

How do I fix this issue and install linux-headers-virtual linux-image-virtual packages which have been kept back in Ubuntu Linux LTS version 12.04.2?

If you are running virtual or cloud images, there is no need to get newer enablement stacks and are thus recommended to remain on the original Precise stack. You only need the newer kernel when

1. You need to support a wider variety of hardware on an existing LTS release, the 12.04.2 and newer point releases will ship with an updated kernel and X stack by default.
2. These newer hardware enablement stacks will be comprised of the newer kernel and X stacks from 12.10 (Quantal), 13.04 (Raring), 13.10 (Saucy), and 14.04 (T name TBD).
3. These enablement stacks are only intended for use on x86 hardware at this time.

If you really want to upgrade virtual/cloud images, try:
$ sudo apt-get dist-upgrade
Sample outputs:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following NEW packages will be installed:
  libterm-readkey-perl linux-headers-3.2.0-52 linux-headers-3.2.0-52-virtual
  linux-image-3.2.0-52-virtual
The following packages will be upgraded:
  base-files dosfstools linux-headers-virtual linux-image-virtual
  linux-libc-dev linux-libc-dev:i386 mysql-client-5.5 mysql-server-5.5
  mysql-server-core-5.5
9 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 50.2 MB of archives.
After this operation, 102 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
....
....
..
Searching for GRUB installation directory ... found: /boot/grub
Searching for default file ... found: /boot/grub/default
Testing for an existing GRUB menu.lst file ... found: /boot/grub/menu.lst
Searching for splash image ... none found, skipping ...
Found kernel: /vmlinuz-3.2.0-52-virtual
Found kernel: /vmlinuz-3.2.0-31-virtual
Found kernel: /memtest86+.bin
Replacing config file /run/grub/menu.lst with new version
Updating /boot/grub/menu.lst ... done

Setting up libterm-readkey-perl (2.30-4build3) ...
Setting up mysql-client-5.5 (5.5.32-0ubuntu0.12.04.1) ...
Setting up mysql-server-core-5.5 (5.5.32-0ubuntu0.12.04.1) ...
Setting up mysql-server-5.5 (5.5.32-0ubuntu0.12.04.1) ...
Installing new version of config file /etc/apparmor.d/usr.sbin.mysqld ...
mysql start/running, process 1013
Setting up dosfstools (3.0.12-1ubuntu1.1) ...
Setting up linux-headers-3.2.0-52 (3.2.0-52.78) ...
Setting up linux-headers-3.2.0-52-virtual (3.2.0-52.78) ...
Setting up linux-headers-virtual (3.2.0.52.62) ...
Setting up linux-image-virtual (3.2.0.52.62) ...

You need to reboot the Ubuntu based system, enter:
# reboot

See See LTS 12.04 support and upgrade policy for more information.