STAN 2.6.0
Rafael Campos-Martin
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/STAN |
| Branch: RELEASE_3_6 |
| Last Commit: bce95ec |
| Last Changed Date: 2017-10-30 12:40:20 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | [ ERROR ] | skipped | skipped | |
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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: 68790 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpCD2qxx/xshell10ae811c35a10' 2>&1
ERROR
Loading required package: poilog
Loading required package: parallel
*** caught segfault ***
address 0x360, 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$bidirOptimParams, SEXPemissionPrior = sizeFactors, SEXPeffectivezero = as.numeric(effectiveZero), SEXPconvergence = as.numeric(convergence), SEXPincrementalEM = as.integer(incrementalEM), SEXPclustering = as.integer(clustering), PACKAGE = "STAN")
2: fitHMM(trainRegions, hmm_poilog, sizeFactors = sizeFactors, maxIters = 10)
3: eval(expr, envir, enclos)
4: eval(expr, envir, enclos)
5: withVisible(eval(expr, envir, enclos))
6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
9: evaluate_call(expr, parsed$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::evaluate(...)
11: 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$render, options))
12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
13: block_exec(params)
14: call_block(x)
15: process_group.block(group)
16: process_group(group)
17: 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$get("infile"), ") ") })
18: process_file(text, output)
19: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv())
20: engine$weave(file, quiet = quiet, encoding = enc)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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)})
25: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...