The problem is caused by the incorrect added sources to Cydia.
The solution is first to download Cyfix GUI from cydia.This program will remove the problematic and incorrect sources from cydia. but you need to first identify the incorrect sources.
To identify the incorrect sources you need to do SSH into your device using Winscp (freeware) or use ifile which don't require pc.
(this method uses Winscp to determine the incorrect sources)
1.open Winscp and type your devices IP address ion Host name section.
2.Type "root" in user name section and "alpine" in password section and press login.
3.go to the directory /private/etc/apt/sources.list.d/ and find Cydia.list
4. open this file with notepad or double click on it. now you will see something like this:
deb
Welcome to Cydia.hackulo.us! ./
deb
Index of / ./
deb
Homepage of repo.beyoip.com ./
deb
http://cydia.*************/ ./
deb
HackStor Repository - MyRepoSpace.com ./
deb
http://cydia.iphonecake.com/ ./
deb http://iphonecake.com/Cydia ./ ----->this is wrong address
Don't forget that you might have something different but all of the sources must like the ones above one except the one that is written wrong address.
Now since you determined the wrong address copy it and put it into Cyfix GUI and press fix. Repeat this to remove all the sources and Respring your device before you open up your Cydia.
(it took me 1 day and half plus learning 5 types of commands for fix mine but this one is the easiest why but i found out the hard way. Hope it will be helpful)