snort использует устаревший xml формат альтернатив. Хочется уже раз и навсегда избьавиться от него в Сизифе. http://www.sisyphus.ru/srpm/Sisyphus/snort/repocop
кроме того, /usr/sbin/snort в пакет паковать не надо. warn snort-2.4.5-alt3.x86_64 file /usr/sbin/snort is alternative in package: snort-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-clamav+flexresp-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-clamav-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-inline+flexresp-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-inline-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-mysql+flexresp-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-mysql-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-odbc+flexresp-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-odbc-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-plain+flexresp-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-snmp+flexresp-2.4.5-alt3.x86_64; file /usr/sbin/snort is alternative in package: snort-snmp-2.4.5-alt3.x86_64;
Исправлено в Cизифе snort-2.4.5-alt4 (xml не до конца подчищен, будет в свежей сборке)