Error(s) in re-building vignettes:
  ...
--- re-building 'DengueVignette.Rmd' using rmarkdown
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

The following object is masked from 'package:phangorn':

    AICc

The following object is masked from 'package:treespace':

    .render.server.info

--- finished re-building 'DengueVignette.Rmd'

--- re-building 'TransmissionTreesVignette.Rmd' using rmarkdown
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

Attaching package: 'igraph'

The following objects are masked from 'package:ape':

    edges, mst, ring

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
treespace
 --- call from context --- 
findMRCIs(tree1)
 --- call from argument --- 
if (class(wiw) != "matrix") stop("The who infected whom information supplied should be of class matrix.")
 --- R stacktrace ---
where 1: findMRCIs(tree1)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 11: 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$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
    engine$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 26: tools:::.buildOneVignette("TransmissionTreesVignette.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/treespace.Rcheck/vign_test/treespace", 
    TRUE, FALSE, "TransmissionTreesVignette", "UTF-8", "/tmp/RtmpilbbMF/file38ec7a776155.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (wiw) 
{
    if (class(wiw) != "matrix") 
        stop("The who infected whom information supplied should be of class matrix.")
    wiwCopy <- matrix(0, nrow(wiw), 2)
    wiwNames <- unique(c(wiw[, 1], wiw[, 2]))
    wiwCopy[, 1] <- match(wiw[, 1], wiwNames)
    wiwCopy[, 2] <- match(wiw[, 2], wiwNames)
    wiw <- wiwCopy
    initial <- min(wiw)
    if (initial == 0) {
        wiw <- wiw + 1
        initial <- min(wiw)
    }
    l <- max(wiw)
    DirectDesc <- lapply(initial:l, function(x) {
        wiw[which(wiw[, 1] == x), 2]
    })
    numDDs <- sapply(DirectDesc, length)
    AllDesc <- lapply(initial:l, function(x) {
        DDs <- DirectDesc[[x]]
        tmpNumDDs <- length(DDs)
        allDs <- rep(NA, length(initial:l))
        allDs[[1]] <- x
        while (tmpNumDDs != 0) {
            allDs[which(is.na(allDs))[1:tmpNumDDs]] <- DDs
            DDs <- do.call(c, DirectDesc[DDs])
            tmpNumDDs <- length(DDs)
        }
        return(allDs[!is.na(allDs)])
    })
    M <- matrix(0, nrow = l, ncol = l)
    for (tmp in initial:l) {
        for (i in AllDesc[[tmp]]) {
            M[tmp, i] <- M[i, tmp] <- tmp
        }
        tmpDDs <- DirectDesc[[tmp]]
        numTmpDDs <- length(tmpDDs)
        if (numTmpDDs > 1) {
            pairs <- combn2(tmpDDs)
            for (j in 1:length(pairs[, 1])) {
                M[AllDesc[[pairs[j, 1]]], AllDesc[[pairs[j, 2]]]] <- M[AllDesc[[pairs[j, 
                  2]]], AllDesc[[pairs[j, 1]]]] <- tmp
            }
        }
    }
    diag(M) <- initial:l
    if (min(M) == 0) {
        warning("No single source case; returning source of longest transmission chain")
        transChainLengths <- sapply(AllDesc, function(x) length(x))
        sourceOfLongestChain <- which(transChainLengths == max(transChainLengths))
        sourceCase <- sourceOfLongestChain
    }
    else {
        sourceCase <- NA
        count <- 1
        while (is.na(sourceCase)) {
            isSource <- setequal(AllDesc[[count]], initial:l)
            if (isSource) {
                sourceCase <- count
            }
            count <- count + 1
        }
    }
    depths <- rep(NA, l)
    count <- 0
    depths[[sourceCase]] <- count
    SCdescs <- unlist(DirectDesc[[sourceCase]], FALSE, FALSE)
    while (length(SCdescs) != 0) {
        count <- count + 1
        depths[SCdescs] <- count
        SCdescs <- unlist(DirectDesc[SCdescs], FALSE, FALSE)
    }
    D <- matrix(ncol = l, nrow = l, depths[M])
    M <- matrix(ncol = l, nrow = l, wiwNames[M])
    colnames(M) <- rownames(M) <- colnames(D) <- rownames(D) <- wiwNames
    return(list(sourceCase = wiwNames[[sourceCase]], mrcis = M, 
        mrciDepths = D))
}
<bytecode: 0x20076378>
<environment: namespace:treespace>
 --- function search by body ---
Function findMRCIs in namespace treespace has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building 'introduction.Rmd' using rmarkdown

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

The following object is masked from 'package:treespace':

    .render.server.info


Attaching package: 'adegraphics'

The following objects are masked from 'package:ade4':

    kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
    s.label, s.logo, s.match, s.traject, s.value, table.value,
    triangle.class

The following object is masked from 'package:ape':

    zoom

--- finished re-building 'introduction.Rmd'

--- re-building 'tipCategories.Rmd' using rmarkdown
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
Loading required package: pander
--- finished re-building 'tipCategories.Rmd'

SUMMARY: processing the following file failed:
  'TransmissionTreesVignette.Rmd'

Error: Vignette re-building failed.
Execution halted