Please provide, as suggested in the comments, information about your system, including what version of the package you have installed. Looking at the current version in github, and as mentioned in the comments, the function read.transcript.features() has been deprecated. However, the replacement function, readTranscriptFeatures() cannot be found in the methylKit package, but in the Bioconductor package genomation. Since in your posted error message you didn't get the deprecation message (see below), I am guessing you have an earlier version of the package. Probably it is better that you have the latest release version installed.
#' @rdname genomation-deprecated
#' @aliases read.transcript.features
message("Use functions in genomation package from Bioconductor\n",
"See vignette for examples.")}