This part is exactly the problem I was talking about:
root@ubuntu-server:~# apt-get update
...
Could not connect to security.ubuntu.com:80 (91.189.92.23). - connect (111: Connection refused) Cannot initiate the connection to security.ubuntu.com:80 (2620:2d:4000:1::102). - connect (101: Network is unreachable) <long line snipped>
<snip>
W: Failed to fetch http://security.ubuntu.com/ubuntu/dists/questing-security/InRelease Cannot initiate the connection to security.ubuntu.com:80 (2620:2d:4000:1::102). - connect (101: Network is unreachable) <long line snipped>
W: Some index files failed to download. They have been ignored, or old ones used instead.
Well... in this case the output does show the failure to connect to 91.189.92.23, but that looks like a different kind of message to the "W:" lines, so maybe it doesn't show up on all setups or didn't make it into the logs on disk, or got buried under other output.If you look at just the W: lines, it mentions a v6 address but the machine doesn't have v6 and the actual problem is the Connection Refused to the v4 address. The output is understandably misleading but ultimately the problem here has nothing to do with v6.
> ...ultimately the problem here has nothing to do with v6.
I agree... more or less. The remainder of this message is a reply to nyrikki, but I'm sticking it under your comment because you might also appreciate how weird it looks like this guy's setup is.
nyrikki: The rest of this message is directed directly at you:
============================
Actually, what's up with your link-local addresses? They have really odd flags on them.
The only way I can figure that you got into that configuration was to remove the kernel-generated link-local address and add a new one with the arguments 'scope link noprefixroute'. Even if a router on your network advertised a fe80::/64 prefix, that does nothing at all, as hosts are supposed to [0] ignore advertised prefixes that are link-local.
Yeah. After playing around with this for a bit, I can see that your network is at either least as misconfigured as one would be if -say- your DHCP server was giving leases with an invalid default gateway, or it is very, very specially configured for very special reasons.
Starting with the ubuntu-server host in the "IPv4 traffic is REJECTed" configuration from my last comment, we do this on the host to delete the kernel-supplied link-local address and instruct the OS to create an address in the link-local address space that can be used for global addresses.
We then configure our upstream router to either* Send RAs on the local link without a prefix
or
* Send RAs on the local link with a link-local prefix (so they're ignored by the Ubuntu host)
or we hard-code the address of a next-hop router on our host. One (or more) of these three things sets up the host with a default route. If you do none of them, you don't get a default route, and global traffic goes nowhere.
Then -because either you or something running on the host deleted the kernel-provisioned link-local address, and then explicitly instructed the kernel to create a link-local address that can be used to reach global addresses- the local host starts emitting IPv6 traffic with a link-local source address and a global destination address.
When presented with this sort of traffic, my router immediately sends back a ICMP6 "destination unreachable, beyond scope", which immediately terminates the connection attempt on the host, so the behavior ends up being exactly the same as when the host didn't have a misconfigured link-local address. But. You claim to be having trouble.
So, there are one or more things that might be going on that explain your trouble.
1) You have a firewall on this host that is dropping important ICMP6 traffic, causing it to miss the "this destination address is beyond your scope" message from the router. Do. Not. Do. This. ICMP is network-management traffic which tells you important things. Dropping important ICMP traffic is how you have mysterious and annoying failures.
2) Your router is configured to ignore link-local traffic with non-link-local destination addresses, rather than replying that the destination is out of scope. On the one hand, this seems stupid to me, but on the other hand, we got here through a misconfiguration that seems very unlikely to me to happen often, [1] so the router admin might not have thought about it when making "locked down" firewall rules.
3) There's some middlebox on the path to the router that's dropping your traffic because not all that many folks would expect to see link-local source and global destination, and middleboxes are widely known for dropping stuff that's even a little bit abnormal.
Investigating your misconfigured host (and maybe also connected network) has been interesting. I'd love to try to figure out if SystemD can be misconfigured to produce the host configuration that we're seeing (or if this misconfiguration is 100% bespoke), but I hear a hot burrito calling my name. Maybe I'll get bored and do more investigation later.
Also, you might object to my conclusion with "But this couldn't happen on IPv4! Clearly IPv6 is too complicated!". I would reply with "What would happen if your host couldn't get a lease from a DHCPv4 server, autoconfigured an address in the IPv4 link-local (169.254.0.0/16) address range, and the network's upstream router was configured to silently drop traffic from that subnet? At least the IPv6 link-local address range is prohibited from sending traffic off the local link [2] and fails the transmission attempt immediately."
[0] ...and Ubuntu questing does ignore such prefixes...
[1] ...that is, a link-local address that has been configured to handle global traffic...
[2] ...unless -as we've discovered- you specifically tell the OS otherwise...