Good night! It has taken me all day to get cocos2d and opencv to play nice on the iphone. First I couldn't link the files with the iphone project from opencv (static libraries). Finally, I found this beautiful post. It helped me compile opencv for iphone really quick. Once that was done, I had to remove a few of the problems that cocos2d has with opencv. Anything that XCode complained about, I stripped out of the opencv source. Most of it was highgui calls. Once that was done, I was able to link the libraries. However, I then could not include the opencv headers in my project!!
I fixed this by realizing opencv has a problem with .mm files. So, once I changed the class I am using opencv in to a .m file, cocos2d played nice with it.