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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 GeneExpressionSignature
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* checking for file ‘GeneExpressionSignature/DESCRIPTION’ ... OK
* preparing ‘GeneExpressionSignature’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 71281 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmph3TtKe/xshell11408774cbecd' 2>&1
 ERROR
--- re-building ‘GeneExpressionSignature.Rmd’ using rmarkdown
Loading required package: GEOquery
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Rows: 33699 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): ID_REF, VALUE, ABS_CALL

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

 *** caught segfault ***
address 0x7fc76ffffff8, cause 'memory not mapped'

Traceback:
 1: vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,     col_types = col_types, id = id, skip = skip, col_select = col_select,     name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws,     escape_double = escape_double, escape_backslash = escape_backslash,     comment = comment, skip_empty_rows = skip_empty_rows, locale = locale,     guess_max = guess_max, n_max = n_max, altrep = vroom_altrep(altrep),     num_threads = num_threads, progress = progress)
 2: vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types,     col_select = {        {            col_select        }    }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max,     na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows,     trim_ws = trim_ws, escape_double = TRUE, escape_backslash = FALSE,     locale = locale, guess_max = guess_max, show_col_types = show_col_types,     progress = progress, altrep = lazy, num_threads = num_threads)
 3: read_tsv(paste(tbltxt, collapse = "\n"), comment = "!sample_table_end",     guess_max = 10000, na = .na_strings)
 4: .parseGSMTxt(txt)
 5: parseGSM(fname)
 6: parseGEO(filename, GSElimits, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL)
 7: getGEO(filename = system.file("extdata/GSM118721.soft", package = "GeneExpressionSignature"))
 8: eval(expr, envir, enclos)
 9: eval(expr, envir, enclos)
10: withVisible(eval(expr, envir, enclos))
11: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
12: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
13: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
14: evaluate_call(expr, parsed$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)
15: evaluate::evaluate(...)
16: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$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$render, options))
17: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
18: eng_r(options)
19: block_exec(params)
20: call_block(x)
21: process_group.block(group)
22: process_group(group)
23: 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$get("infile"),             ") ")    })
24: process_file(text, output)
25: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
26: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
27: vweave_rmarkdown(...)
28: engine$weave(file, quiet = quiet, encoding = enc)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: 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)))})
33: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...