Yes, they are affected by spell resistance
Even though those spell-like abilities, elemental ray and acidic ray, have no spell to base themselves on, spells (in general) and spell-like abilities are subject to spell resistance, unless otherwise noted.
Spells from the conjuration school can mostly ignore spell resistance, and spell-like abilities based on those spells follow the same rules. So a spell-like ability that duplicates Create Pit, which ignores spell resistance, would also ignore spell resistance. This can be seen on the topic When Spell Resistance Applies:
Effect Spells: Most effect spells summon or create something and are not subject to spell resistance. Sometimes, however, spell resistance applies to effect spells, usually to those that act upon a creature more or less directly, such as web.
But spell-like abilities that do not duplicate a spell (like elemental ray and acidic ray) follow a more general rule, with their spell level based on the highest spell the character can cast, as per this FAQ on SLA's:
Cleric domains, sorcerer bloodlines, wizard schools, and certain other class features give spell-like abilities that aren't based on spells. What's the effective spell level for these abilities?
The effective spell level for these spell-like abilities is equal to the highest-level spell that a character of that class could normally cast at the level the ability is gained.
For example, a 1st-level elemental bloodline sorcerer has elemental ray as a spell-like ability. Because a sorcerer 1's highest-level spell available is 1st, that spell-like ability counts as a 1st-level spell. A 9th-level elemental bloodline sorcerer has elemental blast as a spell-like ability. Because a sorcerer 9's highest-level spell available is 4th, that spell-like ability counts as a 4th-level spell.