There are many, many packages with a trim() function. So unfortunately, this question is almost impossible to answer without seeing your code, including the code in your utilities.R script. (If you decide to copy the code here, don't forget to make it look pretty! Helps your helpers a lot 
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This next bit is a totally wild guess (since I don't have enough info to know what's going on), but in case it helps...
One reason why the error might persist after you've commented out the line that sources utilities.R is that later lines are probably still calling functions inside utilities.R (which in turn call the mysterious trim()), and those functions may still be loaded into your global environment. Have you tried commenting out the line that sources utilities.R, then clearing the workspace and restarting R? (this will almost certainly cause other errors, but the interesting question is whether you still see the error involving trim()).