title: Multiple Definition error caused by Atmel Studio 6 linker
body: <p>I am having an issue with Atmel Studio 6.1 where I can not compile due to multiple definition errors, this seems to be caused by the linker duplication "Libraries/lib_mcu/can/can_isp_protocol.o Libraries/lib_mcu/can/can_isp_protocol.o" Does anyone know why it might be doing this? Below is a listing of the compiler output.</p>
  
  <pre><code>    Task "RunCompilerTask"
      C:\Program Files (x86)\Atmel\Atmel Studio 6.1\shellUtils\make.exe all 
      Building file: ../Libraries/lib_mcu/can/can_drv.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "Libraries/lib_mcu/can/can_drv.d" -MT"Libraries/lib_mcu/can/can_drv.d" -MT"Libraries/lib_mcu/can/can_drv.o"   -o "Libraries/lib_mcu/can/can_drv.o" "../Libraries/lib_mcu/can/can_drv.c"
      Finished building: ../Libraries/lib_mcu/can/can_drv.c
      Building file: ../Libraries/lib_mcu/can/can_isp_protocol.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "Libraries/lib_mcu/can/can_isp_protocol.d" -MT"Libraries/lib_mcu/can/can_isp_protocol.d" -MT"Libraries/lib_mcu/can/can_isp_protocol.o"   -o "Libraries/lib_mcu/can/can_isp_protocol.o" "../Libraries/lib_mcu/can/can_isp_protocol.c"
      Finished building: ../Libraries/lib_mcu/can/can_isp_protocol.c
      Building file: ../Libraries/lib_mcu/can/reduced_can_lib.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "Libraries/lib_mcu/can/reduced_can_lib.d" -MT"Libraries/lib_mcu/can/reduced_can_lib.d" -MT"Libraries/lib_mcu/can/reduced_can_lib.o"   -o "Libraries/lib_mcu/can/reduced_can_lib.o" "../Libraries/lib_mcu/can/reduced_can_lib.c"
      Finished building: ../Libraries/lib_mcu/can/reduced_can_lib.c
      Building file: ../Libraries/lib_mcu/eeprom/eeprom_lib.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "Libraries/lib_mcu/eeprom/eeprom_lib.d" -MT"Libraries/lib_mcu/eeprom/eeprom_lib.d" -MT"Libraries/lib_mcu/eeprom/eeprom_lib.o"   -o "Libraries/lib_mcu/eeprom/eeprom_lib.o" "../Libraries/lib_mcu/eeprom/eeprom_lib.c"
      Finished building: ../Libraries/lib_mcu/eeprom/eeprom_lib.c
      Building file: ../Libraries/lib_mcu/flash/flash_boot_drv.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "Libraries/lib_mcu/flash/flash_boot_drv.d" -MT"Libraries/lib_mcu/flash/flash_boot_drv.d" -MT"Libraries/lib_mcu/flash/flash_boot_drv.o"   -o "Libraries/lib_mcu/flash/flash_boot_drv.o" "../Libraries/lib_mcu/flash/flash_boot_drv.c"
      Finished building: ../Libraries/lib_mcu/flash/flash_boot_drv.c
      Building file: ../Libraries/lib_mcu/flash/flash_boot_lib.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "Libraries/lib_mcu/flash/flash_boot_lib.d" -MT"Libraries/lib_mcu/flash/flash_boot_lib.d" -MT"Libraries/lib_mcu/flash/flash_boot_lib.o"   -o "Libraries/lib_mcu/flash/flash_boot_lib.o" "../Libraries/lib_mcu/flash/flash_boot_lib.c"
      Finished building: ../Libraries/lib_mcu/flash/flash_boot_lib.c
      Building file: ../Libraries/lib_module/isp/isp_lib.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "Libraries/lib_module/isp/isp_lib.d" -MT"Libraries/lib_module/isp/isp_lib.d" -MT"Libraries/lib_module/isp/isp_lib.o"   -o "Libraries/lib_module/isp/isp_lib.o" "../Libraries/lib_module/isp/isp_lib.c"
      Finished building: ../Libraries/lib_module/isp/isp_lib.c
      Building file: .././main_can_bootloader_example.c
      Invoking: AVR/GNU C Compiler : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe"  -funsigned-char -funsigned-bitfields -DDEBUG  -I".." -I"../Libraries" -I"../Libraries/lib_board" -I"../Libraries/lib_mcu" -I"../Libraries/lib_mcu/can" -I"../Libraries/lib_mcu/eeprom" -I"../Libraries/lib_mcu/flash" -I"../Libraries/lib_module/isp"  -Os -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -mrelax -g2 -Wall -mmcu=at90can128 -c -std=gnu99 -MD -MP -MF "main_can_bootloader_example.d" -MT"main_can_bootloader_example.d" -MT"main_can_bootloader_example.o"   -o "main_can_bootloader_example.o" ".././main_can_bootloader_example.c"
      Finished building: .././main_can_bootloader_example.c
      Building target: CAN-Bootloader.elf
      Invoking: AVR/GNU Linker : 3.4.2
      "C:\Program Files (x86)\Atmel\Atmel Toolchain\AVR8 GCC\Native\3.4.2.939\avr8-gnu-toolchain\bin\avr-gcc.exe" -o CAN-Bootloader.elf  Libraries/lib_mcu/can/can_drv.o Libraries/lib_mcu/can/can_isp_protocol.o Libraries/lib_mcu/can/can_isp_protocol.o Libraries/lib_mcu/can/reduced_can_lib.o Libraries/lib_mcu/eeprom/eeprom_lib.o Libraries/lib_mcu/flash/flash_boot_drv.o Libraries/lib_mcu/flash/flash_boot_lib.o Libraries/lib_module/isp/isp_lib.o Libraries/lib_module/isp/isp_lib.o main_can_bootloader_example.o   -Wl,-Map="CAN-Bootloader.map" -Wl,--start-group -Wl,-lm  -Wl,--end-group -Wl,--gc-sections -mrelax -Wl,-section-start=.text=0x1e000  -mmcu=at90can128 
  </code></pre>