Code inspector cannot find include files in cross compile project

I have created an example project based on Yocto. I can compile it with the provided cross compiler but the code inspector keeps on finding errors with some include files. This is my toolchain file:

set(CMAKE_SYSTEM_NAME Linux)
set(CMAKE_SYSTEM_PROCESSOR armv7-a)

set(TOOLCHAIN_PREFIX /opt/fsl-imx-fb/4.1.15-2.0.0/sysroots/x86_64-pokysdk-linux/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-)
set(CMAKE_C_COMPILER ${TOOLCHAIN_PREFIX}gcc)
set(CMAKE_CXX_COMPILER ${TOOLCHAIN_PREFIX}g++)

set(CMAKE_SYSROOT /opt/fsl-imx-fb/4.1.15-2.0.0/sysroots/cortexa9hf-neon-poky-linux-gnueabi)

set(CMAKE_PREFIX_PATH ${CMAKE_SYSROOT}/usr/lib/cmake)
set(OE_QMAKE_PATH_EXTERNAL_HOST_BINS /opt/fsl-imx-fb/4.1.15-2.0.0/sysroots/{QT_BIN_PATH})

set(CMAKE_FIND_ROOT_PATH ${CMAKE_SYSROOT})
set(CMAKE_FIND_ROOT_PATH_MODE_PROGRAM NEVER)
set(CMAKE_FIND_ROOT_PATH_MODE_LIBRARY ONLY)
set(CMAKE_FIND_ROOT_PATH_MODE_INCLUDE ONLY)

set(COMPILER_FLAGS " -march=armv7-a -marm -mfpu=neon -mfloat-abi=hard -mcpu=cortex-a9")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${COMPILER_FLAGS}" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${COMPILER_FLAGS}" CACHE STRING "" FORCE)

And this is my source file:
#include <stdio.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
#include <sys/ioctl.h>
#include <linux/types.h>
#include <linux/spi/spidev.h>
#include <stdint.h>
#include <stdio.h>
#include <string.h>
#include <errno.h>

int main(int argc, char **argv)
{
char *name;
int fd;
struct spi_ioc_transfer xfer[2];
unsigned char buf[32], *bp;
int len, status;

name = argv[1];
fd = open(name, O_RDWR);
if (fd < 0) {
perror("open");
return 1;
}

memset(xfer, 0, sizeof xfer);
memset(buf, 0, sizeof buf);
len = sizeof buf;

/*
* Send a GetID command
*/
buf[0] = 0x9f;
len = 6;
xfer[0].tx_buf = (unsigned long)buf;
xfer[0].len = 1;

xfer[1].rx_buf = (unsigned long) buf;
xfer[1].len = 6;

status = ioctl(fd, SPI_IOC_MESSAGE(2), xfer);
if (status < 0) {
perror("SPI_IOC_MESSAGE");
return -1;
}

printf("response(%d): ", status);
for (bp = buf; len; len--) {
printf("%02x ", *bp++);
}
printf("\n");

return 0;
}


I'm getting errors on open/perror/ioctl and printf. But oddly enough not on struct spi_ioc_transfer.
Can anybody help me with pointers on where to look? It is compiling but I would like to use CLion for it's full features.

Best regards,

Jeroen van der Laan