I installed all dependency packages using standard packages. The conflicting libary has been installed using the command
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sudo apt-get install libx264-dev
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pi@raspberrypi ~/HandBrake-0.10.0/build $ make
/usr/bin/g++ -pipe -Wl,-S -fmessage-length=0 -Wall -g0 -O3 -DUSE_X265 -I./libhb/ -I./contrib/include -o HandBrakeCLI -Wl,--start-group test/test.o test/parsecsv.o ./libhb/libhandbrake.a -L./contrib/lib -lass -lavcodec -lavformat -lavutil -lavresample -ldvdnav -ldvdread -lfontconfig -lfribidi -lmp3lame -logg -lsamplerate -lswscale -lvpx -ltheoraenc -ltheoradec -lvorbis -lvorbisenc -lx264 -lbluray -lfreetype -lxml2 -lbz2 -lz -lfdk-aac -lx265 -lpthread -ldl -lm -Wl,--end-group
./contrib/lib/libx265.a(threadpool.cpp.o): In function `x265::ThreadPoolImpl::pokeIdleThread()':
threadpool.cpp:(.text+0x1d4): undefined reference to `__sync_val_compare_and_swap_8'
./contrib/lib/libx265.a(threadpool.cpp.o): In function `x265::PoolThread::threadMain()':
threadpool.cpp:(.text+0x30c): undefined reference to `__sync_or_and_fetch_8'
./contrib/lib/libx265.a(threadpool.cpp.o): In function `x265::ThreadPoolImpl::markThreadAsleep(int)':
threadpool.cpp:(.text+0x410): undefined reference to `__sync_or_and_fetch_8'
./contrib/lib/libx265.a(wavefront.cpp.o): In function `x265::WaveFront::findJob(int)':
wavefront.cpp:(.text+0xe0): undefined reference to `__sync_val_compare_and_swap_8'
./contrib/lib/libx265.a(wavefront.cpp.o): In function `x265::WaveFront::enqueueRow(int)':
wavefront.cpp:(.text+0x274): undefined reference to `__sync_or_and_fetch_8'
./contrib/lib/libx265.a(wavefront.cpp.o): In function `x265::WaveFront::enableRow(int)':
wavefront.cpp:(.text+0x2c4): undefined reference to `__sync_or_and_fetch_8'
./contrib/lib/libx265.a(wavefront.cpp.o): In function `x265::WaveFront::dequeueRow(int)':
wavefront.cpp:(.text+0x408): undefined reference to `__sync_val_compare_and_swap_8'
collect2: ld returned 1 exit status
../test/module.rules:7: recipe for target 'HandBrakeCLI' failed
make: *** [HandBrakeCLI] Error 1