Error(s) in re-building vignettes:
  ...
--- re-building ‘converting_data.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
vcfR
 --- call from context --- 
extract.gt(x)
 --- call from argument --- 
if (class(x@gt) != "matrix") {
    stop(paste("gt slot expected to be of class matrix. Instead found class", 
        class(x@gt)))
}
 --- R stacktrace ---
where 1: extract.gt(x)
where 2: vcfR2genind(vcf)
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 13: block_exec(params)
where 14: call_block(x)
where 15: process_group.block(group)
where 16: process_group(group)
where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 18: process_file(text, output)
where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 21: vweave_rmarkdown(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 27: tools:::.buildOneVignette("converting_data.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vcfR.Rcheck/vign_test/vcfR", 
    TRUE, FALSE, "converting_data", "UTF-8", "/home/hornik/tmp/scratch/Rtmpl28sod/file638e74f0fc8f.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (x, element = "GT", mask = FALSE, as.numeric = FALSE, 
    return.alleles = FALSE, IDtoRowNames = TRUE, extract = TRUE, 
    convertNA = TRUE) 
{
    if (class(x) != "chromR" & class(x) != "vcfR") {
        stop("Expected an object of class chromR or vcfR")
    }
    if (class(x) == "vcfR") {
        if (length(mask) == 1 && mask == TRUE) {
            mask <- FALSE
        }
    }
    if (class(x) == "chromR") {
        tmpMask <- x@var.info$mask
        x <- x@vcf
    }
    if (length(mask) > 1) {
        tmpMask <- mask
        mask <- TRUE
    }
    if (class(x@gt) != "matrix") {
        stop(paste("gt slot expected to be of class matrix. Instead found class", 
            class(x@gt)))
    }
    if (as.numeric == TRUE & return.alleles == TRUE) {
        stop("Invalid parameter choice, as.numeric and return.alleles can't both be true, alleles are characters!")
    }
    if (class(x) == "vcfR") {
        if (colnames(x@gt)[1] != "FORMAT") {
            stop("First column is not named 'FORMAT', this is essential information.")
        }
        outM <- .extract_GT_to_CM(x@fix, x@gt, element, return.alleles, 
            as.integer(extract), convertNA = as.numeric(convertNA))
    }
    if (as.numeric == TRUE) {
        outM <- .CM_to_NM(outM)
    }
    if (IDtoRowNames == TRUE) {
        if (sum(is.na(x@fix[, "ID"])) > 0) {
            x <- addID(x)
        }
        if (length(unique(x@fix[, "ID"])) != nrow(x@fix)) {
            stop("ID column contains non-unique names")
        }
        rownames(outM) <- x@fix[, "ID"]
    }
    if (mask == TRUE) {
        outM <- outM[tmpMask, ]
    }
    return(outM)
}
<bytecode: 0x5653f2af2a00>
<environment: namespace:vcfR>
 --- function search by body ---
Function extract.gt in namespace vcfR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building ‘intro_to_vcfR.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
vcfR
 --- call from context --- 
extract.gt(x, element = "GT")
 --- call from argument --- 
if (class(x@gt) != "matrix") {
    stop(paste("gt slot expected to be of class matrix. Instead found class", 
        class(x@gt)))
}
 --- R stacktrace ---
where 1: extract.gt(x, element = "GT")
where 2: gt.to.popsum(x)
where 3: system.time(x <- gt.to.popsum(x))
where 4: proc.chromR(chrom, verbose = TRUE)
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: withVisible(eval(expr, envir, enclos))
where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 14: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 20: process_file(text, output)
where 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 22: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 23: vweave_rmarkdown(...)
where 24: engine$weave(file, quiet = quiet, encoding = enc)
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 29: tools:::.buildOneVignette("intro_to_vcfR.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vcfR.Rcheck/vign_test/vcfR", 
    TRUE, FALSE, "intro_to_vcfR", "UTF-8", "/home/hornik/tmp/scratch/Rtmpl28sod/file638ea4a640c.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (x, element = "GT", mask = FALSE, as.numeric = FALSE, 
    return.alleles = FALSE, IDtoRowNames = TRUE, extract = TRUE, 
    convertNA = TRUE) 
{
    if (class(x) != "chromR" & class(x) != "vcfR") {
        stop("Expected an object of class chromR or vcfR")
    }
    if (class(x) == "vcfR") {
        if (length(mask) == 1 && mask == TRUE) {
            mask <- FALSE
        }
    }
    if (class(x) == "chromR") {
        tmpMask <- x@var.info$mask
        x <- x@vcf
    }
    if (length(mask) > 1) {
        tmpMask <- mask
        mask <- TRUE
    }
    if (class(x@gt) != "matrix") {
        stop(paste("gt slot expected to be of class matrix. Instead found class", 
            class(x@gt)))
    }
    if (as.numeric == TRUE & return.alleles == TRUE) {
        stop("Invalid parameter choice, as.numeric and return.alleles can't both be true, alleles are characters!")
    }
    if (class(x) == "vcfR") {
        if (colnames(x@gt)[1] != "FORMAT") {
            stop("First column is not named 'FORMAT', this is essential information.")
        }
        outM <- .extract_GT_to_CM(x@fix, x@gt, element, return.alleles, 
            as.integer(extract), convertNA = as.numeric(convertNA))
    }
    if (as.numeric == TRUE) {
        outM <- .CM_to_NM(outM)
    }
    if (IDtoRowNames == TRUE) {
        if (sum(is.na(x@fix[, "ID"])) > 0) {
            x <- addID(x)
        }
        if (length(unique(x@fix[, "ID"])) != nrow(x@fix)) {
            stop("ID column contains non-unique names")
        }
        rownames(outM) <- x@fix[, "ID"]
    }
    if (mask == TRUE) {
        outM <- outM[tmpMask, ]
    }
    return(outM)
}
<bytecode: 0x5608ecd2dbe0>
<environment: namespace:vcfR>
 --- function search by body ---
Function extract.gt in namespace vcfR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building ‘vcf_data.Rmd’ using rmarkdown
--- finished re-building ‘vcf_data.Rmd’

--- re-building ‘workflow.Rmd’ using rmarkdown
--- finished re-building ‘workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘converting_data.Rmd’ ‘intro_to_vcfR.Rmd’

Error: Vignette re-building failed.
Execution halted