/usr/share/vala-0.40/vapi/gdk-3.0.deps is in valac-0.40-vapi 0.40.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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gio-2.0 gdk-pixbuf-2.0 cairo pango pangocairo