user693: I have set up Eclipse to compile for the Arduino Due using all the tools shipped with the Arduino IDE 1.5.6-r2. It compiles without errors, but when uploaded, the Arduino does nothing, and isn't recognized on the computer. It then has to be reset manually using the erase and reset buttons.
There is one static library (ArduinoDueCore) consisting of the Arduino library (core), and other code (Atmel found in lib). The other Eclipse project is the TestProject. It contains one file blinking an LED on pin 13. All the files from the Arduino library are there.
This is the output from Eclipse compiling the library itself: (excerpt of only one of each type of command)
18:31:36 **** Build of configuration Release for project ArduinoDueCore ****
make all
Building file: ../src/lib/variants/arduino_due_x/variant.cpp
Invoking: ARM Sourcery Linux GCC C++ Compiler
arm-none-eabi-g++ -DUSB_PRODUCT="Arduino Due" -DARDUINO=156 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/lib/variants/arduino_due_x/variant.o.lst" -fno-exceptions -fno-rtti -w -c -g -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -MMD -MP -MF"src/lib/variants/arduino_due_x/variant.d" -MT"src/lib/variants/arduino_due_x/variant.d" -mcpu=cortex-m3 -mthumb -o "src/lib/variants/arduino_due_x/variant.o" "../src/lib/variants/arduino_due_x/variant.cpp"
Finished building: ../src/lib/variants/arduino_due_x/variant.cpp

Building file: ../src/lib/libsam/source/adc.c
Invoking: ARM Sourcery Linux GCC C Compiler
arm-none-eabi-gcc -DARDUINO=156 -DARM_MATH_CM3 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PRODUCT="Arduino Due" -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/lib/libsam/source/adc.o.lst" -w -c -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -std=c99 -MMD -MP -MF"src/lib/libsam/source/adc.d" -MT"src/lib/libsam/source/adc.d" -mcpu=cortex-m3 -mthumb -o "src/lib/libsam/source/adc.o" "../src/lib/libsam/source/adc.c"
Finished building: ../src/lib/libsam/source/adc.c

Building file: ../src/core/USB/HID.cpp
Invoking: ARM Sourcery Linux GCC C++ Compiler
arm-none-eabi-g++ -DUSB_PRODUCT="Arduino Due" -DARDUINO=156 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/core/USB/HID.o.lst" -fno-exceptions -fno-rtti -w -c -g -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -MMD -MP -MF"src/core/USB/HID.d" -MT"src/core/USB/HID.d" -mcpu=cortex-m3 -mthumb -o "src/core/USB/HID.o" "../src/core/USB/HID.cpp"
Finished building: ../src/core/USB/HID.cpp

Building file: ../src/core/cortex_handlers.c
Invoking: ARM Sourcery Linux GCC C Compiler
arm-none-eabi-gcc -DARDUINO=156 -DARM_MATH_CM3 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PRODUCT="Arduino Due" -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/core/cortex_handlers.o.lst" -w -c -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -std=c99 -MMD -MP -MF"src/core/cortex_handlers.d" -MT"src/core/cortex_handlers.d" -mcpu=cortex-m3 -mthumb -o "src/core/cortex_handlers.o" "../src/core/cortex_handlers.c"
Finished building: ../src/core/cortex_handlers.c

18:31:39 Build Finished (took 2s.811ms)

Here is the project itself:
18:33:42 **** Build of configuration Release for project TestProject ****
make all
Building file: ../src/TestProject.cpp
Invoking: ARM Sourcery Linux GCC C++ Compiler
arm-none-eabi-g++ -DARDUINO=156 -DUSB_PRODUCT="Arduino Due" -DARDUINO_SAM_DUE -D__SAM3X8E__ -DARDUINO_ARCH_SAM -Dprintf=iprintf -DF_CPU=84000000L -DUSB_MANUFACTURER="Unknown" -DUSB_VID=0x2341 -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/TestProject/src" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -Os -ffunction-sections -fdata-sections -Wall -fno-exceptions -fno-rtti -c -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -g -w -MMD -MP -MF"src/TestProject.d" -MT"src/TestProject.d" -mcpu=cortex-m3 -mthumb -o "src/TestProject.o" "../src/TestProject.cpp"
Finished building: ../src/TestProject.cpp

Building target: TestProject.elf
Invoking: ARM Sourcery Linux GCC C++ Linker
arm-none-eabi-g++ -T"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x/linker_scripts/gcc/flash.ld" -L"/home/kim/workspace_juno/ArduinoDueCore/Release" -Wl,-Map,TestProject.map -lm -lgcc  -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--warn-unresolved-symbols -Wl,--gc-sections -mcpu=cortex-m3 -mthumb -o "TestProject.elf" -Wl,--start-group  ./src/TestProject.o   -lArduinoDueCore -Wl,--end-group
Finished building target: TestProject.elf

make --no-print-directory post-build
/home/kim/arduino-1.5.6-r2/hardware/tools/g++_arm_none_eabi/bin/arm-none-eabi-objcopy -O binary TestProject.elf TestProject.bin

Invoking: ARM Sourcery Linux GNU Create Listing
arm-none-eabi-objdump -h -S TestProject.elf > "TestProject.lst"
Finished building: TestProject.lst

Invoking: ARM Sourcery Linux GNU Print Size
arm-none-eabi-size  --format=berkeley TestProject.elf
   text    data     bss     dec     hex filename
  10396      24    1188   11608    2d58 TestProject.elf
Finished building: TestProject.siz


18:33:43 Build Finished (took 308ms)

Here is the upload command: (removed readWord, go, write and writeWord lines)
-i -d --port=ttyACM0 -U true -e -w -v -b ${project_loc}/Release/${project_name}.bin -R

Set binary mode
chipId=0x285e0a60
Connected at 921600 baud
Erase flash
Write 10420 bytes to flash

[                              ] 0% (0/41 pages)
[=======                       ] 24% (10/41 pages)
[==============                ] 48% (20/41 pages)
[=====================         ] 73% (30/41 pages)
[============================= ] 97% (40/41 pages)
[==============================] 100% (41/41 pages)
Verify 10420 bytes of flash

[                              ] 0% (0/41 pages)
[=======                       ] 24% (10/41 pages)
[==============                ] 48% (20/41 pages)
[=====================         ] 73% (30/41 pages)
[============================= ] 97% (40/41 pages)
[==============================] 100% (41/41 pages)
Verify successful
Set boot flash true
Device       : ATSAM3X8
Chip ID      : 285e0a60
version()=v1.1 Dec 15 2010 19:25:04
Version      : v1.1 Dec 15 2010 19:25:04
Address      : 524288
Pages        : 2048
Page Size    : 256 bytes
Total Size   : 512KB
Planes       : 2
Lock Regions : 32
Locked       : none
Security     : false
Boot Flash   : true
CPU reset.

TestProject.cpp:
#include "Arduino.h"

void setup() {
    pinMode(13, OUTPUT);
}

void loop() {
    digitalWrite(13, HIGH);
    delay(50);
    digitalWrite(13, LOW);
    delay(950);
}


user1310: Using 1.5.6-r2 with Eclipse cause the Due to hung in Default_Handler function after entering main and polling a few times for the next SysTick gettin passed.
Some weak symbol declarations are done twice (i.e. the SysTick_Handler function definitions). They appear to overwrite each others weak alias depending on the link time usage of the objects. All declarations (not only the failing SysTick_Hanlder) from cortex_handler.c are getting overwritten by weak symbol redeclaration inside startup_sam3xa.c.
This commit seems to already address a weak symbol definition problem.
https://github.com/arduino/Arduino/commit/65f00a69c74ca0def8d7f1d7597327945a04a33f
For now, to fix it. Just comment out the part in startup_sam3xa.c with the weak symbol declaration regarding the vectors. Lines 53 to 129.
It should also work to just remove the file completely.
The startup handler code and vector map should be provided by gcc arm built-in libraries instead.

693: <p>I have set up Eclipse to compile for the Arduino Due using all the tools shipped with the Arduino IDE 1.5.6-r2. It compiles without errors, but when uploaded, the Arduino does nothing, and isn't recognized on the computer. It then has to be reset manually using the erase and reset buttons.</p>

<p>There is one static library (ArduinoDueCore) consisting of the Arduino library (<code>core</code>), and other code (Atmel found in <code>lib</code>). The other Eclipse project is the TestProject. It contains one file blinking an LED on pin 13. All the files from the Arduino library are there.</p>

<p>This is the output from Eclipse compiling the library itself: (excerpt of only one of each type of command)</p>

<pre><code>18:31:36 **** Build of configuration Release for project ArduinoDueCore ****
make all
Building file: ../src/lib/variants/arduino_due_x/variant.cpp
Invoking: ARM Sourcery Linux GCC C++ Compiler
arm-none-eabi-g++ -DUSB_PRODUCT="Arduino Due" -DARDUINO=156 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/lib/variants/arduino_due_x/variant.o.lst" -fno-exceptions -fno-rtti -w -c -g -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -MMD -MP -MF"src/lib/variants/arduino_due_x/variant.d" -MT"src/lib/variants/arduino_due_x/variant.d" -mcpu=cortex-m3 -mthumb -o "src/lib/variants/arduino_due_x/variant.o" "../src/lib/variants/arduino_due_x/variant.cpp"
Finished building: ../src/lib/variants/arduino_due_x/variant.cpp

Building file: ../src/lib/libsam/source/adc.c
Invoking: ARM Sourcery Linux GCC C Compiler
arm-none-eabi-gcc -DARDUINO=156 -DARM_MATH_CM3 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PRODUCT="Arduino Due" -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/lib/libsam/source/adc.o.lst" -w -c -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -std=c99 -MMD -MP -MF"src/lib/libsam/source/adc.d" -MT"src/lib/libsam/source/adc.d" -mcpu=cortex-m3 -mthumb -o "src/lib/libsam/source/adc.o" "../src/lib/libsam/source/adc.c"
Finished building: ../src/lib/libsam/source/adc.c

Building file: ../src/core/USB/HID.cpp
Invoking: ARM Sourcery Linux GCC C++ Compiler
arm-none-eabi-g++ -DUSB_PRODUCT="Arduino Due" -DARDUINO=156 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/core/USB/HID.o.lst" -fno-exceptions -fno-rtti -w -c -g -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -MMD -MP -MF"src/core/USB/HID.d" -MT"src/core/USB/HID.d" -mcpu=cortex-m3 -mthumb -o "src/core/USB/HID.o" "../src/core/USB/HID.cpp"
Finished building: ../src/core/USB/HID.cpp

Building file: ../src/core/cortex_handlers.c
Invoking: ARM Sourcery Linux GCC C Compiler
arm-none-eabi-gcc -DARDUINO=156 -DARM_MATH_CM3 -DUSB_MANUFACTURER="Unknown" -DARDUINO_ARCH_SAM -DARDUINO_SAM_DUE -D__SAM3X8E__ -Dprintf=iprintf -DF_CPU=84000000L -DUSB_VID=0x2341 -DUSB_PRODUCT="Arduino Due" -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -Os -ffunction-sections -fdata-sections -Wall -Wa,-adhlns="src/core/cortex_handlers.o.lst" -w -c -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -std=c99 -MMD -MP -MF"src/core/cortex_handlers.d" -MT"src/core/cortex_handlers.d" -mcpu=cortex-m3 -mthumb -o "src/core/cortex_handlers.o" "../src/core/cortex_handlers.c"
Finished building: ../src/core/cortex_handlers.c

18:31:39 Build Finished (took 2s.811ms)
</code></pre>

<p>Here is the project itself:</p>

<pre><code>18:33:42 **** Build of configuration Release for project TestProject ****
make all
Building file: ../src/TestProject.cpp
Invoking: ARM Sourcery Linux GCC C++ Compiler
arm-none-eabi-g++ -DARDUINO=156 -DUSB_PRODUCT="Arduino Due" -DARDUINO_SAM_DUE -D__SAM3X8E__ -DARDUINO_ARCH_SAM -Dprintf=iprintf -DF_CPU=84000000L -DUSB_MANUFACTURER="Unknown" -DUSB_VID=0x2341 -DUSB_PID=0x003E -DUSBCON -I"/home/kim/workspace_juno/ArduinoDueCore/src/core" -I"/home/kim/workspace_juno/TestProject/src" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/libsam" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/CMSIS/Include" -I"/home/kim/workspace_juno/ArduinoDueCore/src/lib/CMSIS/Device/ATMEL/sam3xa/include" -Os -ffunction-sections -fdata-sections -Wall -fno-exceptions -fno-rtti -c -fmessage-length=0 --param max-inline-insns-single=500 -nostdlib -g -w -MMD -MP -MF"src/TestProject.d" -MT"src/TestProject.d" -mcpu=cortex-m3 -mthumb -o "src/TestProject.o" "../src/TestProject.cpp"
Finished building: ../src/TestProject.cpp

Building target: TestProject.elf
Invoking: ARM Sourcery Linux GCC C++ Linker
arm-none-eabi-g++ -T"/home/kim/workspace_juno/ArduinoDueCore/src/lib/variants/arduino_due_x/linker_scripts/gcc/flash.ld" -L"/home/kim/workspace_juno/ArduinoDueCore/Release" -Wl,-Map,TestProject.map -lm -lgcc  -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--warn-unresolved-symbols -Wl,--gc-sections -mcpu=cortex-m3 -mthumb -o "TestProject.elf" -Wl,--start-group  ./src/TestProject.o   -lArduinoDueCore -Wl,--end-group
Finished building target: TestProject.elf

make --no-print-directory post-build
/home/kim/arduino-1.5.6-r2/hardware/tools/g++_arm_none_eabi/bin/arm-none-eabi-objcopy -O binary TestProject.elf TestProject.bin

Invoking: ARM Sourcery Linux GNU Create Listing
arm-none-eabi-objdump -h -S TestProject.elf &gt; "TestProject.lst"
Finished building: TestProject.lst

Invoking: ARM Sourcery Linux GNU Print Size
arm-none-eabi-size  --format=berkeley TestProject.elf
   text    data     bss     dec     hex filename
  10396      24    1188   11608    2d58 TestProject.elf
Finished building: TestProject.siz


18:33:43 Build Finished (took 308ms)
</code></pre>

<p>Here is the upload command: (removed <code>readWord</code>, <code>go</code>, <code>write</code> and <code>writeWord</code> lines)</p>

<pre><code>-i -d --port=ttyACM0 -U true -e -w -v -b ${project_loc}/Release/${project_name}.bin -R

Set binary mode
chipId=0x285e0a60
Connected at 921600 baud
Erase flash
Write 10420 bytes to flash

[                              ] 0% (0/41 pages)
[=======                       ] 24% (10/41 pages)
[==============                ] 48% (20/41 pages)
[=====================         ] 73% (30/41 pages)
[============================= ] 97% (40/41 pages)
[==============================] 100% (41/41 pages)
Verify 10420 bytes of flash

[                              ] 0% (0/41 pages)
[=======                       ] 24% (10/41 pages)
[==============                ] 48% (20/41 pages)
[=====================         ] 73% (30/41 pages)
[============================= ] 97% (40/41 pages)
[==============================] 100% (41/41 pages)
Verify successful
Set boot flash true
Device       : ATSAM3X8
Chip ID      : 285e0a60
version()=v1.1 Dec 15 2010 19:25:04
Version      : v1.1 Dec 15 2010 19:25:04
Address      : 524288
Pages        : 2048
Page Size    : 256 bytes
Total Size   : 512KB
Planes       : 2
Lock Regions : 32
Locked       : none
Security     : false
Boot Flash   : true
CPU reset.
</code></pre>

<p>TestProject.cpp:</p>

<pre><code>#include "Arduino.h"

void setup() {
    pinMode(13, OUTPUT);
}

void loop() {
    digitalWrite(13, HIGH);
    delay(50);
    digitalWrite(13, LOW);
    delay(950);
}
</code></pre>
 1310: <p>Using 1.5.6-r2 with Eclipse cause the Due to hung in Default_Handler function after entering main and polling a few times for the next SysTick gettin passed.</p>

<p>Some weak symbol declarations are done twice (i.e. the SysTick_Handler function definitions). They appear to overwrite each others weak alias depending on the link time usage of the objects. All declarations (not only the failing SysTick_Hanlder) from cortex_handler.c are getting overwritten by weak symbol redeclaration inside startup_sam3xa.c.</p>

<p>This commit seems to already address a weak symbol definition problem.
<a href="https://github.com/arduino/Arduino/commit/65f00a69c74ca0def8d7f1d7597327945a04a33f" rel="nofollow">https://github.com/arduino/Arduino/commit/65f00a69c74ca0def8d7f1d7597327945a04a33f</a></p>

<p>For now, to fix it. Just comment out the part in startup_sam3xa.c with the weak symbol declaration regarding the vectors. Lines 53 to 129.</p>

<p>It should also work to just remove the file completely.
The startup handler code and vector map should be provided by gcc arm built-in libraries instead.</p>
