I am a beginner with APE.

I tried to configure it in a virtual box (Ubuntu 10.0.4) with multiple
subdomains in mind from the beginning.

I did not touch ape.conf, but I did change things in Demos/config.js.

One inconsistency - all the descriptions use APE_JSF but the package
contains a folder named ape-jsf.

And the command:
/etc/init.d/aped restart
did not work, it seems it should be
/etc/init.d/ape-server restart

So at the beginning my config looked like this:
APE.Config.baseUrl = 'http://devbuntu/ape-jsf'; //APE JSF
APE.Config.domain = 'auto';
APE.Config.server = 'ape.devbuntu:6969'; //APE server URL

with Apache virtual host:
 Servername devbuntu
 ServerAlias ape.devbuntu
 ServerAlias *.ape.devbuntu

and also /etc/hosts with
127.0.1.1 devbuntu
127.0.1.1 ape.devbuntu
127.0.1.1 0.ape.devbuntu
127.0.1.1 1.ape.devbuntu
....

When I first ran http://devbuntu/ape-jsf/Tools/Check/ I got a security
error in Firebug. I suspected that this is because of cross-domain
problems because it failed to set the document.domain to devbuntu. So
I added
APE.Config.transport = 2;
to use JSONP.

All the tests and Chat and Move demo worked without any problems with
JSONP. I also testd it from the host machine (APE runs in VirtualBox)
with Internet Explorer 8, Chrome and Firefox.

And I noticed a problem - Firefox and Chrome ran the Check tests fine,
but IE8 always just stopped forever at
Running test : Initializing APE Client
and IE threw a yellow "Error occurred" sign with description
"Permission denied".

So I became sad and thought - oh, if IE does not work, then I cannot
use APE with JSONP. I even tried to set domain to devbuntu in ape.conf
and config.js, but it did not help.

But anyway I ran the Demos and was relieved to see that Chat and Move
ran fine in IE8, no JS errors and everything worked as expected!

So it seems there is some problem in the Tools/Check script on IE8 in
JSONP mode. Without subdomain mixing and without transport = 2 all
Tools/Check tests run fine also in IE8. I mean, the following
config.js:
APE.Config.baseUrl = 'http://ape.devbuntu/ape-jsf'; //APE JSF
without transport = 2, and accessing test by link  
http://ape.devbuntu/ape-jsf/Tools/Check/
works fine also in IE8.
Still I prefer to use JSONP, it seems more foolproof for all cases.

I hope APE Team will fix this issue and I hope it will not affect my
own JS code.

Should I be worried about the IE8 Test/Check JSONP problem? Will it
affect me somehow?

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