##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount
###
##############################################################################
##############################################################################


* checking for file ‘recount/DESCRIPTION’ ... OK
* preparing ‘recount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 81540 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmpg1ILUu/xshell1318c71920299' 2>&1
 ERROR
--- re-building ‘recount-quickstart.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'SRP009615-results.knit'

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

 *** caught segfault ***
address 0x0, cause 'unknown'

Traceback:
 1: .recv_any(manager$backend)
 2: .recv_any(manager$backend)
 3: .manager_recv(manager)
 4: .manager_recv(manager)
 5: .collect_result(manager, reducer, progress, BPPARAM)
 6: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,     BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer,     progress.length = length(redo_index))
 7: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS,     ...)
 8: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
 9: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,     BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
10: bplapply(X = ddd, .wrapMapplyNotShared, .FUN = FUN, .MoreArgs = MoreArgs,     BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
11: bplapply(X = ddd, .wrapMapplyNotShared, .FUN = FUN, .MoreArgs = MoreArgs,     BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
12: bpmapply(.railMatChrRegionCov, sampleFiles, mappedPerXM, L, BPPARAM = BPPARAM.railChr,     MoreArgs = list(chr = chr, regs = regions, verbose = verboseLoad))
13: bpmapply(.railMatChrRegionCov, sampleFiles, mappedPerXM, L, BPPARAM = BPPARAM.railChr,     MoreArgs = list(chr = chr, regs = regions, verbose = verboseLoad))
14: FUN(X[[i]], ...)
15: lapply(regs_split, derfinder:::.railMatChrRegion, sampleFiles = sampleFiles,     chr = chr, mappedPerXM = mappedPerXM, L = 1, verbose = verbose,     BPPARAM.railChr = bpparam, verboseLoad = verboseLoad, chrlen = chrlen)
16: lapply(regs_split, derfinder:::.railMatChrRegion, sampleFiles = sampleFiles,     chr = chr, mappedPerXM = mappedPerXM, L = 1, verbose = verbose,     BPPARAM.railChr = bpparam, verboseLoad = verboseLoad, chrlen = chrlen)
17: coverage_matrix("SRP009615", "chrY", regions)
18: system.time(rse_ER <- coverage_matrix("SRP009615", "chrY", regions))
19: eval(expr, envir, enclos)
20: eval(expr, envir, enclos)
21: eval_with_user_handlers(expr, envir, enclos, user_handlers)
22: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
23: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
24: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
25: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
26: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
27: evaluate::evaluate(...)
28: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
29: in_dir(input_dir(), expr)
30: 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$render, options)))
31: eng_r(options)
32: block_exec(params)
33: call_block(x)
34: process_group.block(group)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
37: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
38: process_file(text, output)
39: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
40: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
41: vweave_rmarkdown(...)
42: engine$weave(file, quiet = quiet, encoding = enc)
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch({    engine$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)))})
47: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...