I just got all my parts for my gaming rig, except for my water coolor (corsair h100). I wonder if its safe to turn on my computer just to install the windows and some programs with no fan on the cpu? how long can it run?
It's not safe. It would run long enough to reach its threshold temperature and then motherboard would shut down the pc.
It will happen quickly, not nearly enough time to install windows.
Install stock cooler from the cpu box for the time being.
You CAN'T do that (if you actually care about your new hardware), and regardless, a bit of patience will serve you nicely. You could use the stock cooler, as Bejusek suggested, but just wait until you get the H100. Less work later.