I realize this question was asked about ~2.5 months ago, so the asker may have moved on, but I came across it while searching for an answer to the same issue. So, hopefully, this will be of help to someone out there!
All I really had to do was verify that ALL the paths I was using were actually pointing to something that existed.
Specifically, I was trying to run:
./configure
--prefix=armv7
--disable-ffmpeg --disable-ffplay --disable-ffprobe --disable-ffserver
--enable-avresample --enable-cross-compile
--sysroot="/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS6.0.sdk"
--target-os=darwin
--cc="/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin/gcc"
--extra-cflags="-arch armv7 -mfpu=neon -miphoneos-version-min=6.0"
--extra-ldflags="-arch armv7 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS6.0.sdk -miphoneos-version-min=6.0"
--arch=arm --cpu=cortex-a9 --enable-pic
^ from http://www.tangentsoftworks.com/2012/11/12/how-to-prepare-your-mac-for-ios-development-with-ffmpeg-libraries/
When I couldn't get it to work, I decided to stop being lazy and actually checked the directories listed in the paths: anything that starts with "/Applications/...".
What I found is that I didn't have "iPhoneOS6.0.sdk" (it's referenced above in the paths) installed.
Changing the script to this worked:
./configure
--prefix=armv7
--disable-ffmpeg --disable-ffplay --disable-ffprobe --disable-ffserver
--enable-avresample --enable-cross-compile
--sysroot="/applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS6.1.sdk"
--target-os=darwin --cc="/applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin/gcc"
--extra-cflags="-arch armv7 -mfpu=neon -miphoneos-version-min=6.0"
--extra-ldflags="-arch armv7 -isysroot /applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS6.1.sdk -miphoneos-version-min=6.0"
--arch=arm --cpu=cortex-a9 --enable-pic
In short, just double-check your paths. Hope that helps!
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