How to skip or ignore this removing process so that upgrading can take place

What is the output of:

file /usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile

Thanks

Hi,
This is the output ...

dads@dads-desktop:~$ file /usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile
/usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile: ERROR: cannot open `/usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile' (Not a directory)
dads@dads-desktop:~$

Also pl note that these files do not exist in the specified folders.

Thanks
Rajinder

ok then run:

sudo mkdir -p /usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile

Then rerun the command which made the initial command.

Should be ok

it is not getting created..see the output..
dads@dads-desktop:~$ sudo mkdir -p /usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile
[sudo] password for dads:
mkdir: cannot create directory `/usr/src/linux-headers-2.6.31-20/arch/mips/fw': Not a directory
dads@dads-desktop:~$

regards
Rajinder
--------------------------------------------------------------------

same is the the output with other file also...
dads@dads-desktop:~$ sudo mkdir -p /usr/src/linux-headers-2.6.31-16/drivers/pci/pcie/aer/Makefile
mkdir: cannot create directory `/usr/src/linux-headers-2.6.31-16/drivers/pci/pcie': Not a directory
dads@dads-desktop:~$
what to do next ?
Regards
Rajinder
---------------------------------------------------------------------

Try:

sudo mkdir -p /usr/src/linux-headers-2.6.31-20/arch/mips/fw

here is the output
dads@dads-desktop:~$ sudo mkdir -p /usr/src/linux-headers-2.6.31-20/arch/mips/fw[sudo] password for dads:
mkdir: cannot create directory `/usr/src/linux-headers-2.6.31-20/arch/mips/fw': File exists
dads@dads-desktop:~$

regards
Rajinder

ok try:

sudo mkdir -p /usr/src/linux-headers-2.6.31-16/drivers/pci/pcie

Basically some folders are missing and when the package is removed, it expects the folder to exist and will moan if it's not, the -p option on mkdir tells the OS to make the parent folders of the desired folder if they do not exist.

thus far you are right but the folders exist only those files dont
here is the output
dads@dads-desktop:~$ sudo mkdir -p /usr/src/linux-headers-2.6.31-16/drivers/pci/pcie
[sudo] password for dads:
mkdir: cannot create directory `/usr/src/linux-headers-2.6.31-16/drivers/pci/pcie': File exists
dads@dads-desktop:~$

and ifor your information pcie is a png file and not a directory so things don't proceed further. and we are unable to create it due to problems not best known to me.
Regards
Rajinder.

ok and:

mkdir -p /usr/src/linux-headers-2.6.31-16/drivers/pci/pcie/aer/Makefile

Then you should be good to go (just re-read the question)

I have deleted pcie file and created the new folder with mkdir so there is a dir as follows
usr/src/linux-headers-2.6.31-16/drivers/pci/pcie/aer/Makefile

But could not create
/usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile
As fw is a file which is not getting deleted...
so now even though one is created still there is problem in file 1 as well as file #2
here is the terminal output...
dads@dads-desktop:~$ sudo apt-get autoremove
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  linux-headers-2.6.31-16 linux-headers-2.6.31-20
0 upgraded, 0 newly installed, 2 to remove and 142 not upgraded.
2 not fully installed or removed.
After this operation, 147MB disk space will be freed.
Do you want to continue [Y/n]? y
(Reading database ... 285626 files and directories currently installed.)
Removing linux-headers-2.6.31-16 ...
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/fs/ramfs/Makefile' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/fs/ramfs' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/fs' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/drivers/video/via/Makefile' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/drivers/video/via' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/drivers/video' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/drivers/pci' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16/drivers' not empty so not removed.
dpkg: warning: while removing linux-headers-2.6.31-16, directory '/usr/src/linux-headers-2.6.31-16' not empty so not removed.
Removing linux-headers-2.6.31-20 ...
dpkg: error processing linux-headers-2.6.31-20 (--remove):
 unable to securely remove '/usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile': Not a directory
Errors were encountered while processing:
 linux-headers-2.6.31-20
E: Sub-process /usr/bin/dpkg returned an error code (1)
dads@dads-desktop:~$

you are right but fw file is not getting deleted as mentioned above ...here is the terminal output
one is cleared and other is still pending
ads@dads-desktop:~$ sudo mkdir -p /usr/src/linux-headers-2.6.31-16/fs/ramfs/Makefile
[sudo] password for dads:
dads@dads-desktop:~$ sudo apt-get autoremove
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  linux-headers-2.6.31-20
0 upgraded, 0 newly installed, 1 to remove and 142 not upgraded.
1 not fully installed or removed.
After this operation, 73.3MB disk space will be freed.
Do you want to continue [Y/n]? y
(Reading database ... 274342 files and directories currently installed.)
Removing linux-headers-2.6.31-20 ...
dpkg: error processing linux-headers-2.6.31-20 (--remove):
 unable to securely remove '/usr/src/linux-headers-2.6.31-20/arch/mips/fw/sni/Makefile': Not a directory
Errors were encountered while processing:
 linux-headers-2.6.31-20
E: Sub-process /usr/bin/dpkg returned an error code (1)
dads@dads-desktop:~$
because fw is a file under mips folder and neither i am able to create nor delete this one....looking solution for this problem.
BTW Thanks for one problem we could clear.
Regards
Rajinder

Thanks Actionparsnip...
You gave me the idea and I could do it by moving the files to other location and then created the wanted files with the same path...
I did the installation of program before confirming you that problem is solved
Thanks
Rajinder

Thanks actionparsnip, that solved my question.