first output

r3d-decoder -a encode_v -f london.r3d | ffmpeg -t 0.417 -f rawvideo -pix_fmt gbrp16le -s 2048x1152 -i - -r 23.976 -pix_fmt yuv420p -aspect 640/360 -vf "scale='ceil(iw*sar/2)*2':'ceil(ih/2)*2',pad='max(iw,ceil(ih*(640/360)))':'ceil(ow/(640/360))':'(ow-iw)/2':'(oh-ih)/2':black,scale=640:360,shuffleplanes=1:2:0:3" -c:v libx264 -b:v 700k -c:a libfdk_aac -b:a 128k -g 50 -keyint_min 50 -movflags faststart -y out.mp4
ffmpeg version 2.6.git Copyright (c) 2000-2015 the FFmpeg developers
  built with gcc 4.4.7 (GCC) 20120313 (Red Hat 4.4.7-11)
  configuration: --prefix=/opt/sb4/stage --extra-cflags=-I/opt/sb4/stage/include --extra-ldflags=-L/opt/sb4/stage/lib --extra-libs=-ldl --enable-gpl --enable-nonfree --enable-version3 --enable-libfdk-aac --enable-libx264 --enable-libfreetype
  libavutil      54. 20.100 / 54. 20.100
  libavcodec     56. 26.100 / 56. 26.100
  libavformat    56. 25.101 / 56. 25.101
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5. 12.100 /  5. 12.100
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  3.100 / 53.  3.100
Input #0, rawvideo, from 'pipe:':
  Duration: N/A, start: 0.000000, bitrate: N/A
    Stream #0:0: Video: rawvideo (G3[0][16] / 0x10003347), gbrp16le, 2048x1152, -1463812 kb/s, 25 tbr, 25 tbn, 25 tbc
[Parsed_shuffleplanes_3 @ 0x1c3d720] Cannot map between a subsampled chroma plane and a luma or alpha plane.
[Parsed_shuffleplanes_3 @ 0x1c3d720] Failed to configure input pad on Parsed_shuffleplanes_3
Error opening filters!

snd output

r3d-decoder -a encode_v -f london.r3d | ffmpeg -t 0.417 -f rawvideo -pix_fmt gbrp16le -s 2048x1152 -i - -r 23.976 -aspect 640/360 -vf "scale='ceil(iw*sar/2)*2':'ceil(ih/2)*2',pad='max(iw,ceil(ih*(640/360)))':'ceil(ow/(640/360))':'(ow-iw)/2':'(oh-ih)/2':black,scale=640:360,shuffleplanes=1:2:0:3,format=yuv420p" -c:v libx264 -b:v 700k -c:a libfdk_aac -b:a 128k -g 50 -keyint_min 50 -movflags faststart -y out.mp4
ffmpeg version 2.6.git Copyright (c) 2000-2015 the FFmpeg developers
  built with gcc 4.4.7 (GCC) 20120313 (Red Hat 4.4.7-11)
  configuration: --prefix=/opt/sb4/stage --extra-cflags=-I/opt/sb4/stage/include --extra-ldflags=-L/opt/sb4/stage/lib --extra-libs=-ldl --enable-gpl --enable-nonfree --enable-version3 --enable-libfdk-aac --enable-libx264 --enable-libfreetype
  libavutil      54. 20.100 / 54. 20.100
  libavcodec     56. 26.100 / 56. 26.100
  libavformat    56. 25.101 / 56. 25.101
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5. 12.100 /  5. 12.100
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  3.100 / 53.  3.100
Input #0, rawvideo, from 'pipe:':
  Duration: N/A, start: 0.000000, bitrate: N/A
    Stream #0:0: Video: rawvideo (G3[0][16] / 0x10003347), gbrp16le, 2048x1152, -1463812 kb/s, 25 tbr, 25 tbn, 25 tbc
[Parsed_shuffleplanes_3 @ 0x2ec0840] Cannot map between a subsampled chroma plane and a luma or alpha plane.
[Parsed_shuffleplanes_3 @ 0x2ec0840] Failed to configure input pad on Parsed_shuffleplanes_3
Error opening filters!