I am working on WiMAX module for NS-3. I am using an external library IT++ for OFDM PHY layer operations. I identified the problem when I tried to compile after including the library. Both NS-3 and IT++ library have same named header files channel.h and config.h. Therefore the pre-processor macros (#ifndef, #define) in channel.h and config.h of NS-3 prevent the same named files from IT++ library from being included for compilation. 

As a temporary solution I changed the pre-processor macro definitions in NS-3 files by adding NS3_ in beginning, i.e., I changed 

#ifndef CHANNEL_H
#define CHANNEL_H

to 

#ifndef NS3_CHANNEL_H
#define NS3_CHANNEL_H

and similarly in config.h file.

However there is need to solve this problem permanently since it is not very unlikely that NS-3 developers use some external libraries which have header files conflicting with those of NS-3.

Thanks.