That message implies that your build process is compiling the native C code with the NDK. That used to be an optional part of compiling for android (if you didn't want to use the precompiled .so files that came with the repo...do you have those?). More recently, a pair of developers added a workflow using jcenter to hold the precompiled pd-on-android library. So if you are using Android Studio+gradle, you can specify that as a dependency and it will be added automatically (See the various .gradle files for MobMuPlat as an example).
However, if you wish to modify pd objects (or add externals to your project), you'll need to use the NDK. Is that the case for you? The last time I did that, I had to do it on the command line (Separate from building and running the android code in Android studio), but I hear that more recent versions of Android Studio have better integration with native code and can be set up to run the NDK automatically on app build.