R/test_installation_vsearch.R

In HajkD/LTRpred: De novo functional annotation of retrotransposons

#' @title Helper function to test VSEARCH installation
#' @noRd
test_installation_vsearch <- function() {
    # test if a valid VSEARCH version is installed
    tryCatch({
        sys_out <-
            system("vsearch -v", intern = TRUE)
    }, error = function(e)
        stop(
            "It seems like you don't have VSEARCH installed locally on your machine or the PATH variable to the VSEARCH program is not set correctly. ",
            "Please consult the Installation vignette or https://github.com/torognes/vsearch ufor details on how to install VSEARCH.",
            call. = FALSE
        ))
    
    if (any(stringr::str_detect(sys_out, "vsearch")))
        return(TRUE)
    
}