WARNING: library configuration mismatch when running ffmpeg

Question

well, just typing ffmpeg on command line gives me lots of spam. I'm perfectly comfortable with that till it does not break my files, but... Is there any way to troubleshoot/fix that?

$ ffmpeg 
FFmpeg version 0.6-4:0.6-2ubuntu6, Copyright (c) 2000-2010 the FFmpeg developers
  built on Oct  5 2010 22:35:47 with gcc 4.4.5
  configuration: --extra-version=4:0.6-2ubuntu6 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-gpl --enable-postproc --enable-x11grab --enable-libdc1394 --enable-shared --disable-static
  WARNING: library configuration mismatch
  libavutil   configuration: --extra-version=4:0.6-2ubuntu3+medibuntu1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libdirac --enable-libgsm --enable-libopenjpeg --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-libmp3lame --enable-libfaac --enable-nonfree --enable-gpl --enable-postproc --enable-x11grab --enable-libfaad --enable-libxvid --enable-libx264 --enable-librtmp --enable-libopencore-amrnb --enable-version3 --enable-libopencore-amrwb --enable-version3 --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavcodec  configuration: --extra-version=4:0.6-2ubuntu3+medibuntu1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libdirac --enable-libgsm --enable-libopenjpeg --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-libmp3lame --enable-libfaac --enable-nonfree --enable-gpl --enable-postproc --enable-x11grab --enable-libfaad --enable-libxvid --enable-libx264 --enable-librtmp --enable-libopencore-amrnb --enable-version3 --enable-libopencore-amrwb --enable-version3 --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavformat configuration: --extra-version=4:0.6-2ubuntu6 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-gpl --enable-postproc --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavdevice configuration: --extra-version=4:0.6-2ubuntu6 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-gpl --enable-postproc --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavfilter configuration: --extra-version=4:0.6-2ubuntu6 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-gpl --enable-postproc --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libswscale  configuration: --extra-version=4:0.6-2ubuntu6 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-gpl --enable-postproc --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libpostproc configuration: --extra-version=4:0.6-2ubuntu6 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-vaapi --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-gpl --enable-postproc --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavutil     50.15. 1 / 50.15. 1
  libavcodec    52.72. 2 / 52.72. 2
  libavformat   52.64. 2 / 52.64. 2
  libavdevice   52. 2. 0 / 52. 2. 0
  libavfilter    1.19. 0 /  1.19. 0
  libswscale     0.11. 0 /  0.11. 0
  libpostproc   51. 2. 0 / 51. 2. 0

$ uname -a
Linux arcano 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 17:40:48 UTC 2011 i686 GNU/Linux

Solution

It's a warning, not an error.

Some of your ffmpeg packages (the medibuntu ones) are older than the updated ones from maverick-updates. This can cause problems as ABIs change.

Three options for avoiding a mismatch:

1. Purge out the Medibuntu packages and go back to pure Ubuntu packages (you might lose some codec options).
2. Set the version of the now updated packages back to the approximate medibuntu version and lock them so they're not updated again.
3. Or compile it yourself. Not as easy as other things.

Option 2 is probably the easiest with the best results.