This commit fixes the issue arduino#2198:

If an analog input is used and during the sketch modified in a digitalOutput
the pinMode(AX, OUTPUT) isn't sensed because of this line of codes:

wiring_analog.c line 135
// Enable the corresponding channel
	if (ulChannel != latestSelectedChannel) {
		adc_enable_channel( ADC, ulChannel );
		if ( latestSelectedChannel != (uint32_t)-1 )
			adc_disable_channel( ADC, latestSelectedChannel );
		latestSelectedChannel = ulChannel;

The channel is infact enabled only if different from the previous one because
of speed problems.

With my patch:

when pinMode(PIN, OUTPUT) is declared a control about if the pin
is an analog one is done and if so the ADC is released

when pinMode(PIN, INPUT) is declared a control is as well done in order to
enable the ADC.

Author: agdl

hardware/arduino/sam/cores/arduino/wiring_digital.c

@@ -32,6 +32,12 @@ extern void pinMode( uint32_t ulPin, uint32_t ulMode )
 	switch ( ulMode )
     {
         case INPUT:
+	    #if defined __SAM3X8E__ || defined __SAM3X8H__
+	    
+	    if(g_APinDescription[ulPin].ulPinType != NO_ADC)
+	           adc_enable_channel( ADC, g_APinDescription[ulPin].ulADCChannelNumber);
+	    #endif
+
             /* Enable peripheral for clocking input */
             pmc_enable_periph_clk( g_APinDescription[ulPin].ulPeripheralId ) ;
             PIO_Configure(
@@ -52,6 +58,12 @@ extern void pinMode( uint32_t ulPin, uint32_t ulMode )
         break ;
 
         case OUTPUT:
+	    #if defined __SAM3X8E__ || defined __SAM3X8H__
+	    
+	    if(g_APinDescription[ulPin].ulPinType != NO_ADC)
+	           adc_disable_channel( ADC, g_APinDescription[ulPin].ulADCChannelNumber);
+	    #endif
+
             PIO_Configure(
             	g_APinDescription[ulPin].pPort,
             	PIO_OUTPUT_1,