BioC 3.4: BUILD report for msPurity on morelia

Package: msPurity

Version: 0.99.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data msPurity

StartedAt: 2016-09-20 02:18:14 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 02:19:10 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 55.7 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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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 msPurity
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* checking for file ‘msPurity/DESCRIPTION’ ... OK
* preparing ‘msPurity’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 15006 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpV3VKQk/xshell3a926765dd80' 2>&1
 ERROR

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

Traceback:
 1: .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x7ffc92c1f620>,     dll = list(name = "Rcpp", path = "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = <pointer: 0x7ffc92c1a660>,         info = <pointer: 0x1007b30c0>), numParameters = -1L),     <pointer: 0x7ffc92e8a790>, <pointer: 0x7ffc92e856f0>, .pointer,     ...)
 2: object@backend$getPeakList(x)
 3: FUN(X[[i]], ...)
 4: lapply(X = X, FUN = FUN, ...)
 5: sapply(scans, function(x) object@backend$getPeakList(x)$peaks,     simplify = FALSE)
 6: sapply(scans, function(x) object@backend$getPeakList(x)$peaks,     simplify = FALSE)
 7: .local(object, ...)
 8: mzR::peaks(mr)
 9: mzR::peaks(mr)
10: .fun(piece, ...)
11: (function (i) {    piece <- pieces[[i]]    if (.inform) {        res <- try(.fun(piece, ...))        if (inherits(res, "try-error")) {            piece <- paste(utils::capture.output(print(piece)),                 collapse = "\n")            stop("with piece ", i, ": \n", piece, call. = FALSE)        }    }    else {        res <- .fun(piece, ...)    }    progress$step()    res})(2L)
12: .Call(loop_apply_, as.integer(n), f, env)
13: loop_apply(n, do.ply)
14: llply(.data = pieces, .fun = .fun, ..., .progress = .progress,     .inform = .inform, .parallel = .parallel, .paropts = .paropts)
15: plyr::alply(files, 1, function(x) {    mr <- mzR::openMSfile(x)    scan_peaks <- mzR::peaks(mr)    return(scan_peaks)})
16: getscans(filepths)
17: purityX(xset, offsets = c(0.5, 0.5), xgroups = c(1, 2))
18: eval(expr, envir, enclos)
19: eval(expr, envir, enclos)
20: withVisible(eval(expr, envir, enclos))
21: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
22: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
23: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler)
24: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
25: in_dir(opts_knit$get("root.dir") %n% input_dir(), evaluate(code,     envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options)))
26: block_exec(params)
27: call_block(x)
28: process_group.block(group)
29: process_group(group)
30: 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$get("infile"),             ") ")    })
31: process_file(text, output)
32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,     encoding = encoding)
33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv())
34: vweave_rmarkdown(...)
35: engine$weave(file, quiet = quiet, encoding = enc)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: 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)})
40: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...