This was due to the Collaboration application that is installed. I have managed to work around the issue, so that the site could be brought back, however I recommend contacting the author of that application for further assistance. Here is the full error log:
Mon, 23 May 2016 15:58:32 +0000 (Severity: 3)
50.28.55.154 - http://engineeringwall.com/admin/upgrade/?controller=upgrade&key=6d2e901946187e7ca04dbeaec148953f&mr=JTdCJTIyMCUyMiUzQTMlMkMlMjIxJTIyJTNBJTIyY29sbGFiJTIyJTJDJTIyZXh0cmElMjIlM0ElN0IlMjJsYXN0U3FsSWQlMjIlM0ExJTdEJTdE&mr_error=1
Error : _SCHEME_NOT_PERMITTED
#0 /home/engineer/public_html/applications/collab/Application.php(839): IPS\Http\_Url->request()
#1 /home/engineer/public_html/applications/core/sources/Setup/Upgrade.php(665): IPS\collab\_Application->installJsonData(true)
#2 [internal function]: IPS\core\Setup\_Upgrade->IPS\core\Setup\{closure}('collab')
#3 /home/engineer/public_html/applications/core/sources/Setup/Upgrade.php(274): call_user_func(Object(Closure), 'collab')
#4 /home/engineer/public_html/applications/core/sources/Setup/Upgrade.php(713): IPS\core\Setup\_Upgrade->appLoop(Array, Object(Closure))
#5 [internal function]: IPS\core\Setup\_Upgrade->step3(Array)
#6 /home/engineer/public_html/applications/core/sources/Setup/Upgrade.php(210): call_user_func(Array, Array)
#7 /home/engineer/public_html/applications/core/modules/setup/upgrade/upgrade.php(48): IPS\core\Setup\_Upgrade->process(Array)
#8 [internal function]: IPS\core\modules\setup\upgrade\_upgrade->IPS\core\modules\setup\upgrade\{closure}(Array)
#9 /home/engineer/public_html/system/Helpers/MultipleRedirect/MultipleRedirect.php(71): call_user_func(Object(Closure), Array)
#10 /home/engineer/public_html/applications/core/modules/setup/upgrade/upgrade.php(105): IPS\Helpers\_MultipleRedirect->__construct(Object(IPS\Http\Url), Object(Closure), Object(Closure))
#11 /home/engineer/public_html/system/Dispatcher/Controller.php(94): IPS\core\modules\setup\upgrade\_upgrade->manage()
#12 /home/engineer/public_html/system/Dispatcher/Setup.php(222): IPS\Dispatcher\_Controller->execute()
#13 /home/engineer/public_html/admin/upgrade/index.php(29): IPS\Dispatcher\_Setup->run()
#14 {main}
Please help