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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingleMoleculeFootprinting
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* checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK
* preparing ‘SingleMoleculeFootprinting’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘FootprintCharter.rmd’ using rmarkdown

 *** caught segfault ***
address 0xd0000001f, cause 'memory not mapped'

Traceback:
 1: parallelDist::parDist(x = MethSM_smoothed, method = "euclidean",     threads = 1)
 2: FootprintCharter(MethSM = MethSM, RegionOfInterest = RegionOfInterest,     coverage = 30, k = 16, n = 5, TF.length = c(5, 75), nucleosome.length = c(120,         1000), cytosine.coverage.thr = 5, verbose = TRUE)
 3: eval(expr, envir)
 4: eval(expr, envir)
 5: withVisible(eval(expr, envir))
 6: 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)})
 7: eval(call)
 8: eval(call)
 9: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
10: doWithOneRestart(return(expr), restart)
11: withOneRestart(expr, restarts[[1L]])
12: withRestartList(expr, restarts[-nr])
13: doWithOneRestart(return(expr), restart)
14: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
15: withRestartList(expr, restarts)
16: withRestarts(with_handlers({    for (expr in tle$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)
17: evaluate::evaluate(...)
18: 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$render, options))
19: in_dir(input_dir(), expr)
20: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
21: eng_r(options)
22: block_exec(params)
23: call_block(x)
24: process_group(group)
25: 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)            }        }    })
26: 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)
27: process_file(text, output)
28: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
29: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
30: vweave_rmarkdown(...)
31: engine$weave(file, quiet = quiet, encoding = enc)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch({    engine$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)))})
36: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...