Error(s) in re-building vignettes:
--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

sh: line 1: 45907 Segmentation fault      (core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpKtc32b/working_dir/Rtmpws64UH/fileb1ef496505dc' 2>&1 < '/tmp/RtmpKtc32b/working_dir/Rtmpws64UH/fileb1ef6ba7e5fc'
--- re-building ‘inapplicable.Rmd’ using rmarkdown
Warning in RNGkind("Mersenne-Twister", "Inversion", "Rounding") :
  non-uniform 'Rounding' sampler used

 *** caught segfault ***
address 0xfffffffc0ad0d1d0, cause 'memory not mapped'

Traceback:
 1: MorphyLength(treeEdge[, 1], treeEdge[, 2], morphyObj, inPostorder,     nTaxa)
 2: MorphyTreeLength(tree, morphyObj)
 3: Fitch(random.tree, my.phyDat)
 4: eval(expr, envir, enclos)
 5: eval(expr, envir, enclos)
 6: withVisible(eval(expr, envir, enclos))
 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
13: 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$render, options)))
14: block_exec(params)
15: call_block(x)
16: process_group.block(group)
17: process_group(group)
18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
19: process_file(text, output)
20: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
21: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
22: vweave_rmarkdown(...)
23: engine$weave(file, quiet = quiet, encoding = enc)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch({    engine$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
28: tools:::.buildOneVignette("inapplicable.Rmd", "/data/gannet/ripley/R/packages/tests-devel/TreeSearch.Rcheck/vign_test/TreeSearch",     TRUE, FALSE, "inapplicable", "UTF-8", "/tmp/RtmpKtc32b/working_dir/Rtmpws64UH/fileb1ef680ee497.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘profile-scores.Rmd’ using rmarkdown
--- finished re-building ‘profile-scores.Rmd’

--- re-building ‘profile.Rmd’ using rmarkdown
Warning in RNGkind("Mersenne-Twister", "Inversion", "Rounding") :
  non-uniform 'Rounding' sampler used
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 1012 = 19.365 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 913 = 18.929 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
  Token count 220 = 5.2854 bits @ 0 extra steps; simulating 975 trees to estimate cost of further steps.
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 517 = 13.954 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 1111 = 19.509 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 715 = 17.137 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 814 = 18.192 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 616 = 15.739 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
  Token count 319 = 8.9099 bits @ 0 extra steps; simulating 12025 trees to estimate cost of further steps.
Warning in ICSteps(c(rep(1, a), rep(2, b)), maxIter = m, warn = warn) :
  Will truncate number of iterations at maxIter = 40000
  Token count 418 = 11.717 bits @ 0 extra steps; simulating 40000 trees to estimate cost of further steps.
--- finished re-building ‘profile.Rmd’

SUMMARY: processing the following file failed:
  ‘inapplicable.Rmd’

Error: Vignette re-building failed.
Execution halted