BioC 3.5: BUILD report for STAN on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data STAN
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* checking for file ‘STAN/DESCRIPTION’ ... OK
* preparing ‘STAN’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 88950 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmpek8Jzz/xshell15b17741617bf' 2>&1
 ERROR
Loading required package: poilog
Loading required package: parallel

 *** caught segfault ***
address 0x350, cause 'memory not mapped'

Traceback:
 1: .Call("RHMMFit", SEXPobs = obs, SEXPpi = initProb, SEXPA = transMat,     SEXPemission = emissionParams, SEXPtype = as.character(emission@type),     SEXPdim = D, SEXPregularize = as.numeric(0), SEXPk = as.integer(nStates),     SEXPmaxIters = as.integer(maxIters), SEXPparallel = as.integer(nCores),     SEXPflags = lapply(bdHMM.settings$dirFlags, as.integer),     SEXPstate2flag = as.integer(bdHMM.settings$state2flag), SEXPcouples = as.integer(bdHMM.settings$couples),     SEXPrevop = as.integer(bdHMM.settings$rev.operation), SEXPverbose = as.integer(verbose),     SEXPupdateTransMat = as.integer(updateTransMat), SEXPfixedEmission = emissionProbs,     SEXPbidiroptim = bdHMM.settings$bidirOptimParams, SEXPemissionPrior = sizeFactors,     SEXPeffectivezero = as.numeric(effectiveZero), SEXPconvergence = as.numeric(convergence),     SEXPincrementalEM = as.integer(incrementalEM), PACKAGE = "STAN")
 2: fitHMM(trainRegions, hmm_poilog, sizeFactors = sizeFactors, maxIters = 10)
 3: eval(expr, envir, enclos)
 4: eval(expr, envir, enclos)
 5: withVisible(eval(expr, envir, enclos))
 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
 9: evaluate_call(expr, parsed$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)
10: 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$render,         options))
11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),     stop_on_error = if (options$error && options$include) 0L else 2L,     output_handler = knit_handlers(options$render, options)))
12: block_exec(params)
13: call_block(x)
14: process_group.block(group)
15: process_group(group)
16: 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$get("infile"),             ") ")    })
17: process_file(text, output)
18: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",     file)) knit2pandoc else knit)(file, encoding = encoding,     quiet = quiet, envir = globalenv())
19: engine$weave(file, quiet = quiet, encoding = enc)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) {    stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA, call. = FALSE)})
24: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
BioC 3.5: BUILD report for STAN on veracruz2

Summary

Command output
