%z is the signed offset in hours, in the format hhmm, not hh:mm. Here's one way to remove the last :.
newstring <- gsub("(.*).(..)$","\\1\\2","2013-04-05T07:49:54-07:00")
(timep <- strptime(newstring, "%Y-%m-%dT%H:%M:%S%z", tz="UTC"))
# [1] "2013-04-05 14:49:54 UTC"
Also note that you don't have to remove the "T".
