Inheritance: error in calling the constructor of the base class?
#include "../Adafruit_NeoPixel/Adafruit_NeoPixel.h"
#include "../IRremote/IRremote.h"
#include "../DS3231/DS3231.h"


What you're doing there is telling the compiler where, relative to where it's performing the compiling (or one of its include directories), the header files you list are.

What you're not doing is telling the IDE where the CPP files are to compile and link with your sketch.

When including anything external to the sketch folder that is more than just a header file you must treat it as an Arduino library - that is, place it in one of the standard library folders and name it properly (libraries should be named LibraryName/LibraryName.h).

Then you include the libraries properly:

#include &lt;Adafruit_NeoPixel.h&gt;
#include &lt;IRremote.h&gt;
#include &lt;DS3231.h&gt;


You must do that in both your sketch and your custom library.  That way the IDE knows where to look for the files to compile - the compiler doesn't understand the concept of an Arduino library (and thus the CPP files associated with a header file) - that is purely down to the IDE gathering the data by examining your sketch and locating the right files to then pass to the compiler.