Ok, I've read through this whole thread and I've got to side with the
pro-custom-timeout people. This is friggin ridiculous. Here's another
use case at the opposite end of the spectrum from most of the above:

I have a perfectly good script built around notify-send I was using on
Gentoo. It worked fine there with whatever DNS-compatible notification
daemon I had installed (obviously not NotifyOSD). It's short and simple
- it just watches the log file for a local application server and
notifies me when it has stopped or started.

Build, deploy and server restart cycles can take quite a long time -
often 10-20 minutes plus. During that time I might wander away, or start
doing something in another window, but I absolutely do not want to miss
that notification. If I leave for 5 minutes and the server finishes
restarting while I'm gone I want that notification to still be visible
when I get back. So my notify-send call specified a pretty long duration
(around 10 minutes). This was practical because whichever (superior)
notification system was installed also allowed the user to close
notifications early after they'd been read.

I switched over to Ubuntu a couple weeks ago because I've been running
it on my wife's machines for months and it's grown on me. I've been
pretty happy with it overall - definitely some annoyances but Googling
and liberal use of gconf have generally been enough to work around them.
But I'm trying to get back up to functional parity with what I had in
Gentoo, particularly work-related stuff like this monitor, and I've been
banging my head against this bug/deliberate gimping for hours.

I've installed the patched version of NotifyOSD from the PPA mentioned
above, and it did take care of the timeout issue. But there appears to
be no way for me to kill the notifications before they naturally expire.
So I either run a very good chance of missing the notifications, or I
see them and then they're stuck in the corner of my screen for ten
minutes with no way to clear them. Not going to work.

Several times in this thread it's been suggested that if you don't like
the way NotifyOSD works you should install something else. That's a
pretty ridiculous thing to suggest to developers planning to distribute
their code, but since this is just for my personal use, fine. There
seems to be a problem with that approach though - Synaptic won't let me
uninstall notify-osd without also removing ubuntu-desktop, which seems
like a pretty significant package.

It seems like only one of these notification daemons can run at a time
(which makes sense if they're all reading the same D-Bus messages). I
tried installing notification-daemon without removing notify-osd and the
system just keeps on using the latter. So I'm very confused as to what
I'm expected to do at this point.

If the Ubuntu devs truly think their "alternate interpretation" of the
DNS spec is actually in line with the spec, then why wouldn't I be able
to swap out their daemon for any other compatible daemon and still have
ubuntu-desktop work? If ubuntu-desktop is transmitting proper messages
based on the spec then anything else should be able to display them,
right? Otherwise I don't see how Ubuntu isn't violating the same "don't
assume stuff about the notification server" principle that others in
this thread have used to criticize people complaining about the ignored
-t parameter.

Does anyone know if:

- there's something I can manually edit to remove this dependency so I
can switch to notification-daemon and still keep ubuntu desktop?

- there is a way to run both NotifyOSD for ubuntu-desktop and
notification-daemon for notify-send at the same time? Some way of
telling notify-send to use an alternate D-Bus channel to connect with
notification-daemon or something?

- there is some other simple command to fire simple messages that
actually works in the way I want? I don't care if these notifications
blend in seamlessly with Ubuntu's. I just want something that will pop
up, not steal focus, expire when I decide it should, yet let me manually
close it early. Bear in mind this is an extremely basic script.

This whole situation is disappointing. The beauty of the notification
spec combined with notify-send is that throwing a nice looking GUI
notification is no harder than echoing text to the console, and is just
as cross-distro. Or at least it was up until this point.

-- 
notify-send ignores the expire timeout parameter
https://bugs.launchpad.net/bugs/390508
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