This is most likely to happen when setting one but not the other.
Note that we already warn when rootprefixdir != rootprefix_default,
at the very end.
if not prefixdir.startswith('/')
error('Prefix is not absolute: "@0@"'.format(prefixdir))
endif
+if prefixdir != rootprefixdir and not prefixdir.startswith(rootprefixdir.strip('/') + '/')
+ error('Prefix is not below root prefix (now rootprefix=@0@ prefix=@1@)'.format(
+ rootprefixdir, prefixdir))
+endif
+
bindir = join_paths(prefixdir, get_option('bindir'))
libdir = join_paths(prefixdir, get_option('libdir'))
sysconfdir = join_paths(prefixdir, get_option('sysconfdir'))