BioC 3.6: BUILD report for deepSNV on veracruz1

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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 deepSNV
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* checking for file ‘deepSNV/DESCRIPTION’ ... OK
* preparing ‘deepSNV’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 71061 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmp6ZWEtq/xshell10f5e2dd9251' 2>&1
 ERROR

 *** caught segfault ***
address 0x0, cause 'unknown'

Traceback:
 1: .C("bam2R", as.character(file), as.character(chr), as.integer(start),     as.integer(stop), vector("integer", (stop - start + 1) *         11 * 2), as.integer(q), as.integer(mq), as.integer(s),     as.integer(head.clip), as.integer(max.depth), as.integer(verbose),     as.integer(mask), PACKAGE = "deepSNV")
 2: bam2R(f, regions$chr[j], regions$start[j], regions$stop[j], ...)
 3: FUN(X[[i]], ...)
 4: lapply(X = X, FUN = FUN, ...)
 5: mclapply(files, function(f) {    test.matrix <- matrix(0, ncol = length(nucleotides), nrow = rows)    for (j in 1:nrow(regions)) {        test.matrix[beg[j]:end[j], ] = bam2R(f, regions$chr[j],             regions$start[j], regions$stop[j], ...)[, nucleotides]    }    mode(test.matrix) <- "integer"    test.matrix}, mc.cores = mc.cores)
 6: loadAllData(files, regions, q = 30)
 7: eval(expr, envir, enclos)
 8: eval(expr, envir, enclos)
 9: withVisible(eval(expr, envir, enclos))
10: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
11: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
12: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
13: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
15: 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$render, options)))
16: block_exec(params)
17: call_block(x)
18: process_group.block(group)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
21: process_file(text, output)
22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,     encoding = encoding)
23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv())
24: vweave_rmarkdown(...)
25: engine$weave(file, quiet = quiet, encoding = enc)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch({    engine$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)})
30: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
BioC 3.6: BUILD report for deepSNV on veracruz1

Summary

Command output
