TIMER1 CTC Interrupts not working with avr-gcc

Question

I am attempting to program my arduino in plain C, and I've come across some very strange behavior. If I load the following code from the Arduino IDE, it works as expected and toggles Pin 6 every 100ms. However, if I compile it with avr-gcc and then load it with avrdude, no interrupts are run. Here is the C code:

#include <avr/io.h>
#include <avr/interrupt.h>
int main();
void timer1_init();
int main()
{
 // connect led to pin PD6
 DDRD |= (1 << 6);
 PORTD |= (1 << 6);
 // initialize timer
 timer1_init();
 // loop forever
 while(1)
 {
 // do nothing
 // whenever a match occurs, ISR is fired
 // toggle the led in the ISR itself
 // no need to keep track of any flag bits here
 // done!
 }
}
// initialize timer, interrupt and variable
void timer1_init()
{
 /*cli();*/
 /*TCCR1A = 0;*/
 /*TCCR1B = 0;*/
 /*TCNT1 = 0;*/
 OCR1A = 24999;
 TCCR1B |= _BV(WGM12) | _BV(CS11) | _BV(CS10);
 TIMSK1 |= _BV(OCIE1A);
 sei();
}
ISR (TIMER1_COMPA_vect)
{
 // toggle led here
 PORTD ^= (1 << 6);
}

And here is the Makefile I'm using to load it onto the arduino:

CC = avr-gcc
CFLAGS = -g -O0 -Wall -fno-exceptions -ffunction-sections -fdata-sections -mmcu=atmega328p -DF_CPU=16000000L -MMD -DUSB_VID=null -DUSB_PID=null -DARDUINO=106
SOURCE = test
all: load
$(SOURCE): $(SOURCE).o
 $(CC) $(SOURCE).o -o $(SOURCE)
hex: $(SOURCE)
 avr-objcopy -O ihex -R .eeprom $(SOURCE) $(SOURCE).hex
load: hex
 avrdude -F -V -c arduino -p ATMEGA328P -P /dev/tty.usbmodem1411 -b 115200 -U flash:w:$(SOURCE).hex
clean:
 rm -f *.o *.hex
 rm -f `find . -perm 755 | perl -pe 's/\.\n//g' | perl -pe 's/\.\/(\w+)\n/1円 /g'`

Is there something that the arduino ide automatically adds to it that makes it work? What am I missing?

Edit: Here is the make output:

avr-gcc -g -O0 -Wall -fno-exceptions -ffunction-sections -fdata-sections -mmcu=atmega328p -DF_CPU=16000000L -MMD -DUSB_VID=null -DUSB_PID=null -DARDUINO=106 -c -o test.o test.c
avr-gcc test.o -o test
avr-objcopy -O ihex -R .eeprom test test.hex
avrdude -F -V -c arduino -p ATMEGA328P -P /dev/tty.usbmodem1411 -b 115200 -U flash:w:test.hex
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.01s
avrdude: Device signature = 0x1e950f
avrdude: NOTE: "flash" memory has been specified, an erase cycle will be performed
 To disable this feature, specify the -D option.
 avrdude: erasing chip
 avrdude: reading input file "test.hex"
 avrdude: input file test.hex auto detected as Intel Hex
 avrdude: writing flash (196 bytes):
 Writing | ################################################## | 100% 0.04s
 avrdude: 196 bytes of flash written
 avrdude: safemode: Fuses OK (E:00, H:00, L:00)
 avrdude done. Thank you.

• Ignacio Vazquez-Abrams: Can we see the full make output?
• Gerben: I'd uncomment the lines TCCR1A=0; TCCR1B = 0; TCNT1 = 0;.
• cheshircat: I tried uncommenting them, it didn't change anything
• jfpoilpret: It seems the make output does not match the makefile you posted: how the first avr-gcc got called from your makefile is a mystery to me...
• cheshircat: It's automatically generated from the target "$(SOURCE).o

Answer 1

I just tried using arduino-mk https://github.com/sudar/Arduino-Makefile, and it worked, so I guess I'm just going to stick with that.

• xyz: Personally, I would recommend using a timer library to achieve interrupts. They are object oriented and so much cleaner and memory efficient.
• jfpoilpret: So it was your makefile that was incorrect?
• cheshircat: Yes, it was the makefile
• Chris Stratton: The issue is probably not the Makefile per se, but that your ISR must match the name of something listed in a vectors table in a source file placed in a section placed in the right place by the linker map. Using an arduino-ish Makefile included a setup for such matching the ISR name you used.