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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 bcSeq
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* checking for file ‘bcSeq/DESCRIPTION’ ... OK
* preparing ‘bcSeq’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 31797 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpzdUIGI/xshell75b66b5ebac2' 2>&1
ERROR
--- re-building ‘bcSeq.Rnw’ using knitr
*** caught segfault ***
*** caught segfault ***
*** caught segfault ***
*** caught segfault ***
address 0x8, cause 'memory not mapped'
address 0x8, cause 'memory not mapped'
address 0x8, cause 'memory not mapped'
address 0x8, cause 'memory not mapped'
Traceback:
1: .bcSeq_hamming(sampleFile = sampleFile, libFile = libFile, outFile = outFile, misMatch = misMatch, tMat = tMat, numThread = numThread, count_only = count_only, detail_info = detail_info)
2: bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2, tMat = NULL, numThread = 4, count_only = TRUE)
3: eval(expr, envir, enclos)
Traceback:
1: Warning: stack imbalance in '<-', 45 then 46
4: .bcSeq_hamming(sampleFile = sampleFile, libFile = libFile, outFile = outFile, Warning: stack imbalance in '{', 41 then 39
eval(expr, envir, enclos) misMatch = misMatch, tMat = tMat, numThread = numThread,
count_only = count_only, detail_info = detail_info) 5:
withVisible(eval(expr, envir, enclos)) 2:
bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2, tMat = NULL, 6: numThread = 4, count_only = TRUE)withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler) 3:
withVisible(eval(expr, envir, enclos)) 7:
handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 4: enclos)), warning = wHandler, error = eHandler, message = mHandler))eval(expr, envir, enclos)
8: 5: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, withVisible(eval(expr, envir, enclos)) envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
6: 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, error = eHandler, message = mHandler) debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message, 7: output_handler = output_handler, include_timing = include_timing)handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))10:
evaluate::evaluate(...) 8:
timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 11: envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 9: options$include) 0L else 2L, output_handler = knit_handlers(options$render, evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, options)) debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message, 12: output_handler = output_handler, include_timing = include_timing)in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 10: stop_on_error = if (options$error && options$include) 0L else 2L, evaluate::evaluate(...) output_handler = knit_handlers(options$render, options)))
11: 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), block_exec(params) keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render, 14: options))call_block(x)
12: 15: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, process_group.block(group) keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L, 16: output_handler = knit_handlers(options$render, options)))process_group(group)
13: 17: block_exec(params)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {14: setwd(wd)call_block(x) cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i), 15: collapse = "-"), " (", knit_concord$get("infile"), process_group.block(group) ") ")
})16:
process_group(group)18:
process_file(text, output)17:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 19: error = function(e) {(if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("-", setwd(wd) file)) knit2pandoc else knit)(file, encoding = encoding, cat(res, sep = "\n", file = output %n% "") quiet = quiet, envir = globalenv(), ...) message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"), 20: ") ")engine$weave(file, quiet = quiet, encoding = enc) })
21: 18: doTryCatch(return(expr), name, parentenv, handler)process_file(text, output)
22: 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])(if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\nfile]rst$",
file)) knit2pandoc else knit)(file, encoding = encoding, 23: quiet = quiet, envir = globalenv(), ...)tryCatchList(expr, classes, parentenv, handlers)
20: 24: engine$weave(file, quiet = quiet, encoding = enc)tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)21: setwd(startdir)doTryCatch(return(expr), name, parentenv, handler) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {22: texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)23: }tryCatchList(expr, classes, parentenv, handlers) outputs <- c(outputs, output)
}, error = function(e) {24: thisOK <<- FALSEtryCatch({ fails <<- c(fails, file) engine$weave(file, quiet = quiet, encoding = enc) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", setwd(startdir) file, conditionMessage(e))) output <- find_vignette_product(name, by = "weave", engine = engine)}) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)25: output <- find_vignette_product(name, by = "texi2pdf", tools::buildVignettes(dir = ".", tangle = TRUE)
engine = engine)An irrecoverable exception occurred. R is aborting now ...
} 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)))})
25: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...