Infrared Remote not working with interupts

Im using the arduino mega. Im using the pulse meter (http://pulsesensor.com/pages/code-and-guide) and need to have it working parallel to a IR remote. I think that the Pulse interrupt is overriding the one for the remote. Does anyway one an suggestions on how to fix this?

ISR(TIMER2_COMPA_vect) {                        // triggered when Timer2 counts to 124
  cli();                                      // disable interrupts while we do this
  Signal = analogRead(pulsePin);              // read the Pulse Sensor
  sampleCounter += 2;                         // keep track of the time in mS with this variable
  int N = sampleCounter - lastBeatTime;       // monitor the time since the last beat to avoid noise

  //  find the peak and trough of the pulse wave
  if (Signal < thresh && N > (IBI / 5) * 3) { // avoid dichrotic noise by waiting 3/5 of last IBI
    if (Signal < T) {                       // T is the trough
      T = Signal;                         // keep track of lowest point in pulse wave
    }
  }

  if (Signal > thresh && Signal > P) {        // thresh condition helps avoid noise
    P = Signal;                             // P is the peak
  }                                        // keep track of highest point in pulse wave

  //  NOW IT'S TIME TO LOOK FOR THE HEART BEAT
  // signal surges up in value every time there is a pulse
  if (N > 250) {                                  // avoid high frequency noise
    if ( (Signal > thresh) && (Pulse == false) && (N > (IBI / 5) * 3) ) {
      Pulse = true;                               // set the Pulse flag when we think there is a pulse
      IBI = sampleCounter - lastBeatTime;         // measure time between beats in mS
      lastBeatTime = sampleCounter;               // keep track of time for next pulse

      if (secondBeat) {                      // if this is the second beat, if secondBeat == TRUE
        secondBeat = false;                  // clear secondBeat flag
        for (int i = 0; i <= 9; i++) {       // seed the running total to get a realisitic BPM at startup
          rate[i] = IBI;
        }
      }

      if (firstBeat) {                       // if it's the first time we found a beat, if firstBeat == TRUE
        firstBeat = false;                   // clear firstBeat flag
        secondBeat = true;                   // set the second beat flag
        sei();                               // enable interrupts again
        return;                              // IBI value is unreliable so discard it
      }


      // keep a running total of the last 10 IBI values
      word runningTotal = 0;                  // clear the runningTotal variable

      for (int i = 0; i <= 8; i++) {          // shift data in the rate array
        rate[i] = rate[i + 1];                // and drop the oldest IBI value
        runningTotal += rate[i];              // add up the 9 oldest IBI values
      }

      rate[9] = IBI;                          // add the latest IBI to the rate array
      runningTotal += rate[9];                // add the latest IBI to runningTotal
      runningTotal /= 10;                     // average the last 10 IBI values
      BPM = 60000 / runningTotal;             // how many beats can fit into a minute? that's BPM!
      QS = true;                              // set Quantified Self flag
      // QS FLAG IS NOT CLEARED INSIDE THIS ISR
    }
  }

  if (Signal < thresh && Pulse == true) {  // when the values are going down, the beat is over
    Pulse = false;                         // reset the Pulse flag so we can do it again
    amp = P - T;                           // get amplitude of the pulse wave
    thresh = amp / 2 + T;                  // set thresh at 50% of the amplitude
    P = thresh;                            // reset these for next time
    T = thresh;
  }

  if (N > 2500) {                          // if 2.5 seconds go by without a beat
    thresh = 512;                          // set thresh default
    P = 512;                               // set P default
    T = 512;                               // set T default
    lastBeatTime = sampleCounter;          // bring the lastBeatTime up to date
    firstBeat = true;                      // set these to avoid noise
    secondBeat = false;                    // when we get the heartbeat back
  }
  Temp = Thermistor(analogRead(tempPin));
  Sweat = Moisture();

/**************** ISSUE HERE ***************/
  String input = "";
  if (irrecv.decode(&results)) // have we received an IR signal?
  {
    Serial.println("inside Ir");
    input = translateSelectionIR();
    Serial.println(input);
    irrecv.resume(); // receive the next value
  }

  if (input.equals(REMOTE_SELECT)) {
    Serial.println("inside main menu");
    MainMenu mM;
    mM.displayMainMenu();
  }
/*******************************************/
  sei();                                   // enable interrupts when youre done!
}

You could try this version of IR NEC library.

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