I was trying to do a fresh install of Piwik on my system with php v5.6.30.
The file integrity check at the second step of the wizard is so heavy that never completes effectively preventing the installation of Piwik.
I upped the php execution timeout to 120 seconds and still it never completes. Over that the web server timeout kicks in.
For the records, it appears that the whole files checking appears to run serially in a single php process and not spawing to multiple processes.
For whoever ends up in my same scenario, deleting the config\manifest.inc.php disables the file integrity check and allows the setup wizard to complete.