Maybe the file does not actually exist, and the warning message is somehow not being reported?

> readGT("I_am_not_a_file", "hg19")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'path' for signature '"character"'
In addition: Warning message:
In normalizePath(path.expand(file)) :
  path[1]="I_am_not_a_file": No such file or directory

I guess this would fail: file.exists(vcf).

Below is the output of the proposed experiment - it works with the sample data.  Below that is the output to traceback().

**** experiment ****

> example(readVcf)
> ## ...lots of output,completes normally
> z <- readGT(fl, nucleotides = TRUE)
>​

**** traceback() output ****

!> traceback()
 13: stop(gettextf("unable to find an inherited method for function %s for signature %s",
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
 12: (function (classes, fdef, mtable)
     {
         methods <- .findInheritedMethods(classes, fdef, mtable)
         if (length(methods) == 1L)
             return(methods[[1L]])
         else if (length(methods) == 0L) {
             cnames <- paste0("\"", vapply(classes, as.character,
                 ""), "\"", collapse = ", ")
             stop(gettextf("unable to find an inherited method for function %s for signature %s",
                 sQuote(fdef@generic), sQuote(cnames)), domain = NA)
         }
         else stop("Internal error in finding inherited methods; didn't return a unique method",
             domain = NA)
     })(list("character"), function (object, ...)
     standardGeneric("path"), <environment>)
 11: path(file)
 10: stop("scanVcf: ", conditionMessage(err), "\n  path: ", path(file),
         call. = FALSE)
 9: value[[3L]](cond)
 8: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
        names[nh], parentenv, handlers[[nh]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({
        file <- normalizePath(path.expand(file))
        if (!file.exists(file))
            stop("file does not exist")
        maps <- .vcf_scan_header_maps(file, fixed, info, geno, samples)
        result <- .Call(.scan_vcf_character, file, as.integer(yieldSize),
            maps$samples, maps$fmap, maps$imap, maps$gmap, row.names)
        setNames(result, "*:*-*")
    }, scanTabix_io = function(err) {
        stop("scanVcf: ", conditionMessage(err), call. = FALSE)
    }, error = function(err) {
        stop("scanVcf: ", conditionMessage(err), "\n  path: ", path(file),
            call. = FALSE)
    })
 5: .vcf_scan_character(file, ..., fixed = vcfFixed(param), info = vcfInfo(param),
        geno = vcfGeno(param), samples = vcfSamples(param))
 4: scanVcf(file, param = param, row.names = row.names)
 3: scanVcf(file, param = param, row.names = row.names)
 2: .readLite(file, "GT", param, "GT", row.names = row.names)
 1: readGT(vcf, nucleotides = TRUE)