Having issues to build any sketch for the Zero on IDE 1.6.5-r2. I have the SAMD installed via the Boards Manager. Just trying the basic Blink sketch. I do have verbose checked in preferences.
Arduino: 1.6.5 (Windows XP), Board: "Arduino Zero (Programming Port)"
C:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\tools\arm-none-eabi-gcc\4.8.3-2014q1/bin/arm-none-eabi-g++ -mcpu=cortex-m0plus -mthumb -c -g -Os -w -ffunction-sections -fdata-sections -fno-threadsafe-statics -nostdlib --param max-inline-insns-single=500 -fno-rtti -fno-exceptions -MMD -DF_CPU=48000000L -DARDUINO=10605 -DARDUINO_SAMD_ZERO -DARDUINO_ARCH_SAMD -D__SAMD21G18A__ -DUSB_VID=0x2341 -DUSB_PID=0x804d -DUSBCON -DUSB_MANUFACTURER="Arduino LLC" -DUSB_PRODUCT="Arduino Zero" -IC:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\tools\CMSIS\4.0.0-atmel/CMSIS/Include/ -IC:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\tools\CMSIS\4.0.0-atmel/Device/ATMEL/ -IC:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\hardware\samd\1.6.0\cores\arduino -IC:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\hardware\samd\1.6.0\variants\arduino_zero C:\DOCUME~1\User\LOCALS~1\Temp\build8327364640953901596.tmp\Blink.cpp -o C:\DOCUME~1\User\LOCALS~1\Temp\build8327364640953901596.tmp\Blink.cpp.o
In file included from C:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\hardware\samd\1.6.0\cores\arduino/Uart.h:25:0,
from C:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\hardware\samd\1.6.0\variants\arduino_zero/variant.h:40,
from C:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\hardware\samd\1.6.0\cores\arduino/delay.h:27,
from C:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\hardware\samd\1.6.0\cores\arduino/Arduino.h:75,
from Blink.ino:18:
c:\documents and settings\user\my documents\downloads\arduino\arduino-1.6.5-r2\portable\packages\arduino\tools\arm-none-eabi-gcc\4.8.3-2014q1\arm-none-eabi\include\c++\4.8.3\cstddef:41:28: fatal error: bits/c++config.h: No such file or directory
#include <bits/c++config.h>
^
compilation terminated.
Error compiling.
It looks like it is looking for the /bits/ include files in the wrong place.
This bits folder appears to be empty.
C:\Documents and Settings\User\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\tools\arm-none-eabi-gcc\4.8.3-2014q1\arm-none-eabi\include\bits
I do see the include files a few levels down in:
C:\Documents and Settings\Randal\My Documents\Downloads\Arduino\arduino-1.6.5-r2\portable\packages\arduino\tools\arm-none-eabi-gcc\4.8.3-2014q1\arm-none-eabi\include\c++\4.8.3\arm-none-eabi\bits
If I copy these files to the empty folder above then it will build okay.