"Operation not permitted" while installing linux-headers-4.8.0-45
Solution 1:
I can see that you asked this question a long time ago, so it's probably not relevant to you any more, but I did run into this exact issue recently. Were you by any chance running Sophos Antivirus? That was preventing me from updating. I was able to install everything by temporarily disabling Sophos Antivirus with savdctl disable, then I installed what I needed and then re-enabled savdctl enable.
Solution 2:
This worked for me when I had the same issue
apt autoremove -f