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xcode - Apple Mach-O linker (id) warning : building for MacOSX, but linking against dylib built for iOS

Starting from some point in the past xCode 4 in complaining about linker problems:

ld: warning: building for MacOSX, but linking against dylib built for iOS: /Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator5.0.sdk/System/Library/Frameworks//CoreGraphics.framework/CoreGraphics

I have checked everything but still nothing suspicious in the config and it compiles and runs. The only thing that I see it is double slashes before CoreGraphics.framework, why I do not know. Tried remove and add again library on "Build phases" that did not help.

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Sometimes it's easier to debug Xcode problems by looking at the build log for the command lines it's using.

If you're building from the command line, you can get that message if you don't specify -miphoneos-version-min=

This compiles:
(where conftest.c just contains int main() {})
/Applications/Xcode5.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang -arch i386 --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.0.sdk --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator6.0.sdk -miphoneos-version-min=6.0 conftest.c

And this gives the error:
/Applications/Xcode5.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang -arch i386 --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.0.sdk --sysroot /Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.0.sdk  conftest.c
ld: building for MacOSX, but linking against dylib built for iOS Simulator file '/Applications/Xcode5.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator6.0.sdk/usr/lib/libSystem.dylib' for architecture i386
clang: error: linker command failed with exit code 1 (use -v to see invocation)

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