Error(s) in re-building vignettes:
  ...
--- re-building ‘NetRep.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

 *** caught segfault ***
address 100010, cause 'memory not mapped'
Warning: stack imbalance in 'lazyLoadDBfetch', 86 then 83
Warning: stack imbalance in 'lazyLoadDBfetch', 85 then 84

Traceback:
 1: structure(list(name = name, exit = NULL, handler = handler, description = description,     test = test, interactive = interactive), class = "restart")
 2: makeRestart(handler = spec)
 3: makeRestartList(...)
 4: withRestarts({    .Internal(.signalCondition(simpleWarning(msg, call), msg,         call))    .Internal(.dfltWarn(msg, call))}, muffleWarning = function() NULL)
 5: .signalSimpleWarning("Failed with error:\nBLAS/LAPACK routine 'DORGQRNo transposeCo' gave error code -3\nSkipping to next comparison",     base::quote(value[[3L]](cond)))
 6: warning("Failed with error:\n", e$message, "\nSkipping to next comparison",     immediate. = TRUE)
 7: value[[3L]](cond)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch({    vCat(verbose, 0, sep = "", "Calculating preservation of network subsets from dataset ",         "\"", datasetNames[di], "\"", " in dataset ", "\"", datasetNames[ti],         "\"", ".")    ct <- contingencyTable(moduleAssignments[c(di, ti)], modules[[di]],         nodelist[[ti]])    contingency <- ct$contingency    propVarsPres <- ct$propVarsPres    overlapVars <- ct$overlapVars    varsPres <- ct$varsPres    overlapModules <- ct$overlapModules    overlapAssignments <- ct$overlapAssignments    nStatistics <- ifelse(!is.null(data[[di]]) && !is.null(data[[ti]]),         7, 4)    nModules <- length(overlapModules)    if (di != loadedIdx) {        anyDM <- any.disk.matrix(data[[loadedIdx]], correlation[[loadedIdx]],             network[[loadedIdx]])        vCat(verbose && anyDM, 1, "Unloading dataset from RAM...")        dataEnv$matrix <- NULL        correlationEnv$matrix <- NULL        networkEnv$matrix <- NULL        gc()        anyDM <- any.disk.matrix(data[[di]], correlation[[di]],             network[[di]])        vCat(verbose && anyDM, 1, "Loading matrices of dataset \"",             datasetNames[di], "\" into RAM...", sep = "")        if (!is.null(data[[di]])) {            dataEnv$matrix <- Scale(loadIntoRAM(data[[di]]))            gc()        }        else {            dataEnv$matrix <- NULL        }        correlationEnv$matrix <- loadIntoRAM(correlation[[di]])        networkEnv$matrix <- loadIntoRAM(network[[di]])        loadedIdx <- di    }    vCat(verbose, 1, "Pre-computing network properties in dataset \"",         datasetNames[di], "\"...", sep = "")    if (is.null(data[[di]]) || is.null(data[[ti]])) {        discProps <- IntermediatePropertiesNoData(correlationEnv$matrix,             networkEnv$matrix, nodelist[[ti]], moduleAssignments[[di]],             modules[[di]])    }    else {        discProps <- IntermediateProperties(dataEnv$matrix, correlationEnv$matrix,             networkEnv$matrix, nodelist[[ti]], moduleAssignments[[di]],             modules[[di]])    }    if (ti != loadedIdx) {        anyDM <- any.disk.matrix(data[[loadedIdx]], correlation[[loadedIdx]],             network[[loadedIdx]])        vCat(verbose && anyDM, 1, "Unloading dataset from RAM...")        dataEnv$matrix <- NULL        correlationEnv$matrix <- NULL        networkEnv$matrix <- NULL        gc()        anyDM <- any.disk.matrix(data[[ti]], correlation[[ti]],             network[[ti]])        vCat(verbose && anyDM, 1, "Loading matrices of dataset \"",             datasetNames[ti], "\" into RAM...", sep = "")        if (!is.null(data[[ti]])) {            dataEnv$matrix <- Scale(loadIntoRAM(data[[ti]]))            gc()        }        else {            dataEnv$matrix <- NULL        }        correlationEnv$matrix <- loadIntoRAM(correlation[[ti]])        networkEnv$matrix <- loadIntoRAM(network[[ti]])        loadedIdx <- ti    }    if (is.null(data[[di]]) || is.null(data[[ti]])) {        perms <- PermutationProcedureNoData(discProps, correlationEnv$matrix,             networkEnv$matrix, moduleAssignments[[di]], modules[[di]],             nPerm, nThreads, model, verbose, vCat)    }    else {        perms <- PermutationProcedure(discProps, dataEnv$matrix,             correlationEnv$matrix, networkEnv$matrix, moduleAssignments[[di]],             modules[[di]], nPerm, nThreads, model, verbose, vCat)    }    observed <- perms$observed    if (nPerm > 0) {        nulls <- perms$nulls    }    else {        nulls <- NULL    }    if (nPerm > 0) {        vCat(verbose, 1, "Calculating P-values...")        if (model == "overlap") {            totalSize <- length(overlapVars)        }        else {            totalSize <- ncol(correlation[[ti]])        }        p.values <- permutationTest(nulls, observed, varsPres,             totalSize, alternative)    }    else {        p.values <- NULL        totalSize <- NULL    }    vCat(verbose, 1, "Collating results...")    res[[di]][[ti]] <- list(nulls = nulls, observed = observed,         p.values = p.values, nVarsPresent = varsPres, propVarsPresent = propVarsPres,         totalSize = totalSize, alternative = alternative, contingency = contingency)    res[[di]][[ti]] <- res[[di]][[ti]][!sapply(res[[di]][[ti]],         is.null)]    gc()}, error = function(e) {    warning("Failed with error:\n", e$message, "\nSkipping to next comparison",         immediate. = TRUE)})
11: modulePreservation(network = network_list, data = data_list,     correlation = correlation_list, moduleAssignments = module_labels,     discovery = "cohort1", test = "cohort2", nPerm = 10000, nThreads = 2)
12: eval(expr, envir, enclos)
13: eval(expr, envir, enclos)
14: withVisible(eval(expr, envir, enclos))
15: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
16: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
17: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
18: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
19: evaluate::evaluate(...)
20: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
21: 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$render, options)))
22: block_exec(params)
23: call_block(x)
24: process_group.block(group)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
27: process_file(text, output)
28: knit(input, text = text, envir = envir, quiet = quiet)
29: knit2html(..., force_v1 = TRUE)
30: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",     file)) knit2pandoc else knit)(file, encoding = encoding,     quiet = quiet, envir = globalenv(), ...)
31: vweave(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({    engine$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)))})
37: tools:::buildVignettes(dir = "/home/ripley/R/packages/tests32/NetRep.Rcheck/vign_test/NetRep",     ser_elibs = "/tmp/Rtmp3Qa4lN/file4e5f77563f5.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from lines 245-251 (NetRep.Rmd)