Error(s) in re-building vignettes:
  ...
--- re-building 'phylin_tutorial.Snw' using Sweave
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
phylin
 --- call from context --- 
gen.variogram(r.dist, d.gen)
 --- call from argument --- 
if (class(y) == "list") {
    multi <- TRUE
    for (i in 1:length(y)) {
        if (!(class(y[[i]]) == "dist")) 
            y[[i]] <- as.dist(y[[i]])
        if (!all(dim(y[[i]]) == dim(x))) 
            stop("Dimensions of x and y do not match.")
    }
} else {
    if (!(class(y) == "dist")) 
        y <- as.dist(y)
    if (!all(dim(y) == dim(x))) 
        stop("Dimensions of x and y do not match.")
}
 --- R stacktrace ---
where 1: gen.variogram(r.dist, d.gen)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: 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 20: tools:::.buildOneVignette("phylin_tutorial.Snw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/phylin.Rcheck/vign_test/phylin", 
    TRUE, FALSE, "phylin_tutorial", "UTF-8", "/tmp/RtmpBjGMyo/file21582ac470b2.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x, y, lag = quantile(as.matrix(x), 0.05), tol = lag/2, 
    lmax = NA, bootstraps = 999, verbose = FALSE) 
{
    if (!(class(x) == "dist")) 
        x <- as.dist(x)
    multi <- FALSE
    if (class(y) == "list") {
        multi <- TRUE
        for (i in 1:length(y)) {
            if (!(class(y[[i]]) == "dist")) 
                y[[i]] <- as.dist(y[[i]])
            if (!all(dim(y[[i]]) == dim(x))) 
                stop("Dimensions of x and y do not match.")
        }
    }
    else {
        if (!(class(y) == "dist")) 
            y <- as.dist(y)
        if (!all(dim(y) == dim(x))) 
            stop("Dimensions of x and y do not match.")
    }
    if (multi) {
        gv <- .gen.variogram.multi(x, y, lag = lag, tol = tol, 
            lmax = lmax, bootstraps = bootstraps, verbose = verbose)
    }
    else {
        gv <- .gen.variogram.single(x, y, lag = lag, tol = tol, 
            lmax = lmax)
    }
    if (sum(is.na(gv$gamma)) > 0) {
        warning("The variogram contains NAs.", "Consider adjusting the lag.")
    }
    gv
}
<bytecode: 0x1c93ca8>
<environment: namespace:phylin>
 --- function search by body ---
Function gen.variogram in namespace phylin has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building 'resistance_tutorial.Snw' using Sweave
Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: 'igraph'

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

    union

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

    decompose, spectrum

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

    union

Loading required package: Matrix

Attaching package: 'gdistance'

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

    normalize

Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in gen.variogram(geo.dist, simul.gen.dist, lag = 0.01) :
  The variogram contains NAs.Consider adjusting the lag.
Warning in gen.variogram(res.dist, simul.gen.dist, lag = 120) :
  The variogram contains NAs.Consider adjusting the lag.
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "numeric") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(Coords) == "matrix") { :
  the condition has length > 1 and only the first element will be used
--- finished re-building 'resistance_tutorial.Snw'

SUMMARY: processing the following file failed:
  'phylin_tutorial.Snw'

Error: Vignette re-building failed.
Execution halted