##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data diffuStats
###
##############################################################################
##############################################################################


* checking for file ‘diffuStats/DESCRIPTION’ ... OK
* preparing ‘diffuStats’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘intro.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x150000001e, cause 'memory not mapped'

Traceback:
 1: ParallelHeatrank(K[, bkgd.names], perms, scores.mat)
 2: FUN(X[[i]], ...)
 3: lapply(pieces, .fun, ...)
 4: structure(lapply(pieces, .fun, ...), dim = dim(pieces))
 5: plyr::llply(stats::setNames(names(scores), names(scores)), function(scores.name) {    bkgd.names <- rownames(scores[[scores.name]])    input.names <- colnames(scores[[scores.name]])    if (!all(bkgd.names %in% rownames(K)))         stop("In background ", scores.name, ", some of the input node names ",             "are not found in the kernel! ", "Check that the rownames of the input are ",             "contained in the names of the graph nodes.")    prob <- (sample.prob[[scores.name]])    if (!is.null(prob) & (length(prob) != length(bkgd.names)))         stop("Sampling probabilities have length ", length(prob),             " but the background has, instead, ", length(bkgd.names))    scores.mat <- methods::as(scores[[scores.name]], "sparseMatrix")    max.sample <- max(Matrix::colSums(scores.mat != 0))    message(paste0(scores.name, ": permuting scores..."))    message("Permuting...")    set.seed(seed)    perms <- t(plyr::laply(seq(n.perm), function(dummy) {        sample(x = seq_along(bkgd.names), prob = prob, size = max.sample,             replace = FALSE)    }, .parallel = FALSE))    message(paste0(scores.name, ": computing heatRank..."))    ans <- ParallelHeatrank(K[, bkgd.names], perms, scores.mat)    rownames(ans) <- rownames(K)    colnames(ans) <- input.names    if (oneminusHeatRank)         return(as.matrix(1 - ans))    return(as.matrix(ans))})
 6: diffuse_mc(graph = graph, scores = scores, ...)
 7: diffuStats::diffuse(graph = graph_toy, method = "mc", scores = input_mat)
 8: eval(expr, envir)
 9: eval(expr, envir)
10: withVisible(eval(expr, envir))
11: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
12: eval(call)
13: eval(call)
14: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
15: doWithOneRestart(return(expr), restart)
16: withOneRestart(expr, restarts[[1L]])
17: withRestartList(expr, restarts[-nr])
18: doWithOneRestart(return(expr), restart)
19: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
20: withRestartList(expr, restarts)
21: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
22: evaluate::evaluate(...)
23: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
24: in_dir(input_dir(), expr)
25: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
26: eng_r(options)
27: block_exec(params)
28: call_block(x)
29: process_group(group)
30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (xfun::pkg_available("rlang", "1.0.0")) {            if (is_R_CMD_build() || is_R_CMD_check()) {                cnd = tryCatch(rlang::entrace(e), error = identity)                error <<- format(cnd)            }            else {                rlang::entrace(e)            }        }    })
31: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (xfun::pkg_available("rlang", "1.0.0")) {            if (is_R_CMD_build() || is_R_CMD_check()) {                cnd = tryCatch(rlang::entrace(e), error = identity)                error <<- format(cnd)            }            else {                rlang::entrace(e)            }        }    }), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
32: process_file(text, output)
33: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
34: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
35: vweave_rmarkdown(...)
36: engine$weave(file, quiet = quiet, encoding = enc)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch({    engine$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)))})
41: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...