New answers tagged compatibility
It's mostly games that might be incompatible with x86. Typically, apps have no reason to use the NDK unless they has special performance or graphics requirements, and their libraries might only be built for ARM. I don't believe that apps using root are typically incompatible, it's rooting apps — since they often rely on platform-specific binaries/...
You can't freely copy binaries from your Ubuntu box to emulator one - even if all are x86-based, they use different basic OS libraries. To compile binary for Android-x86 target you must use special cross-compiling tools\environment. See Android sources toolchain to take a look on how they configure gcc+ld switches to create android-x86 binaries on Ubuntu ...
What file(1) utility says about your compiled binary? Because compiling on x86-based PC does not promises your binary always will have x86 target platform - GCC can produce virtually any targets.
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