Error(s) in re-building vignettes:
--- re-building ‘mvgraphnorm-intro.Rnw’ using Sweave
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: mvtnorm
Loading required package: qpgraph
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’

Attaching package: ‘qpgraph’

The following object is masked from ‘package:mvtnorm’:

    rmvnorm

The following object is masked from ‘package:igraph’:

    graph

 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
mvgraphnorm
 --- call from context --- 
.GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
 --- call from argument --- 
if (class(rho) == "matrix") {
    diag(rho) <- 1
    if (!is.positive.definite(rho)) {
        rho <- as.matrix(nearPD(rho, corr = T)$mat)
    }
}
 --- R stacktrace ---
where 1: .GRCM_n(diag_ = bin.mat, rho = cor, method = "HTF")
where 2: .gensample(n = n.samples + nrow(net.str), bin.mat = net.str, 
    method = method[1], cor = cor, mean.vector = mean.vector, 
    m.var = m.var)
where 3: rmvggm(20, net.str = g, method = "htf", cor = m)
where 4: eval(expr, .GlobalEnv)
where 5: eval(expr, .GlobalEnv)
where 6: withVisible(eval(expr, .GlobalEnv))
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 12: evalFunc(ce, options)
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 15: driver$runcode(drobj, chunk, chunkopts)
where 16: utils::Sweave(...)
where 17: engine$weave(file, quiet = quiet, encoding = enc)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: tryCatch({
    engine$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)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 22: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/mvgraphnorm.Rcheck/vign_test/mvgraphnorm", 
    ser_elibs = "/tmp/RtmpA5adls/file79f5ec05d85.rds")

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (diag_, rho = 0, method = "IPF") 
{
    if (class(rho) == "matrix") {
        diag(rho) <- 1
        if (!is.positive.definite(rho)) {
            rho <- as.matrix(nearPD(rho, corr = T)$mat)
        }
    }
    w <- as.matrix(qpG2Sigma(diag_, rho = rho, matrix.completion = method))
    d_d <- diag(diag(w)^(-1/2), nrow(diag_))
    dg <- d_d %*% w %*% d_d
    retval <- list(sigcov = w, sigcor = dg)
    return(retval)
}
<bytecode: 0x277fd128>
<environment: namespace:mvgraphnorm>
 --- function search by body ---
Function .GRCM_n in namespace mvgraphnorm has this body.
 ----------- END OF FAILURE REPORT -------------- 

Error: processing vignette 'mvgraphnorm-intro.Rnw' failed with diagnostics:
 chunk 4 (label = plotunif) 
Error in if (class(rho) == "matrix") { : the condition has length > 1

--- failed re-building ‘mvgraphnorm-intro.Rnw’

SUMMARY: processing the following file failed:
  ‘mvgraphnorm-intro.Rnw’

Error: Vignette re-building failed.
Execution halted