<p>The paper discusses difficulties evinced by students, particularly novices, in studying programming. It focuses on the difficulties that arise from Discipline-Oriented Teaching (DOT) of a programming language, where the aim is not to learn the language for its own sake, but rather to provide limited knowledge of it necessary for carrying out domain-specific tasks. The paper begins with a discussion of the DOT of programming in general and the R programming language in particular, and examines scholarly research on several particular difficulties, to which DOT may lead, as it invites fragmented and shallow teaching, a fast pace, and parrot-fashion. It next presents the first systematic research on students’ difficulties with DOT of R. Carried out in a 14-week R course intended for undergraduates in a Psychology Department and which incorporates various aspects of DOT, the research is based on an analysis of replies obtained from weekly questionnaires. The questionnaires were completed by 63 students who participated in the course. It was found that the aforementioned teaching practices presented various obstacles to students’ successful learning, including forgetting previously taught material, fragmentary knowledge, difficulty in answering non-replication questions, and variation in solution methods. We suggest that the research results should be considered in designing programming courses based on DOT.</p>