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I happened to download a source packages with zip format. When I use makepkg to make a arch package, it goes wrong becase it couldn't run configure. And I found the files in a zip file unpacked by bsdtar lost their mode bits information, but it's ok when unpacked with unzip. So I recommend that makepkg have a config of uncompressing programs.
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Use noextract=() and unzip it yourself.
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