Ubuntu – Will apt-get dist-upgrade upgrade the system to newer version?

You seem to have libc6, udev etc from ppas. Do you? These are just too fundamental for coming from outside ubuntu.

I expect you will have to get rid of these ppas [from sources.list etc] and try again

This also happened to me using 16.04.1 live Ubuntu persistent USB stick.

uncledave's solution didn't work at first, but as suggested, changing the rights was the final solution.

Then I've found answer #11 from daniel-gimpelevich for bug 1601971 The following commands helped me repair apt-get update

sudo chmod -R a+rX,u+w /var/cache/app-info/xapian/default

How did I guess that 755 is the right mask? The difference between

ls -ld /var/cache/app-info/xapian
drwxr-xr-x 1 root root 4096 Nov 19 20:35 /var/cache/app-info/xapian/

and

ls -ld /var/cache/app-info/xapian/default
drw-r--r-- 2 root root 4096 Jul 19 20:54 /var/cache/app-info/xapian/default

After this apt-get update ran fine.

sudo apt-get update
Hit:1 http://archive.ubuntu.com/ubuntu xenial InRelease
Get:2 http://security.ubuntu.com/ubuntu xenial-security InRelease [94.5 kB]
Get:3 http://archive.ubuntu.com/ubuntu xenial-updates InRelease [95.7 kB]      
Fetched 190 kB in 0s (312 kB/s)                                                
Reading package lists... Done

Note1 Upgrading a live persistent USB stick this way is not suggested it will cause issues if too many packages are installed/upgraded.

Note2 It's a better idea to install Ubuntu directly to the USB stick if you want to use it as a bootable "Swiss Army Knife".