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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
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* checking for file ‘recountWorkflow/DESCRIPTION’ ... OK
* preparing ‘recountWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 84780 Bus error: 10 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpNMlIXu/xshelldb3a31ba66a5' 2>&1
ERROR
--- re-building ‘recount-workflow.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
Content type 'binary/octet-stream' length 12604886 bytes (12.0 MB)
==================================================
downloaded 12.0 MB
trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true'
Content type 'application/octet-stream' length 548129 bytes (535 KB)
==================================================
downloaded 535 KB
2024-04-16 11:28:37.103 R[84780:2555538921] XType: com.apple.fonts is not accessible.
2024-04-16 11:28:37.109 R[84780:2555538921] XType: XTFontStaticRegistry is enabled.
[WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata,
e.g. by using --metadata pagetitle="..." on the command line.
Falling back to 'gene_report.knit'
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_exon.Rdata'
Content type 'binary/octet-stream' length 110177449 bytes (105.1 MB)
==================================================
downloaded 105.1 MB
*** caught segfault ***
address 0x2, cause 'memory not mapped'
*** caught segfault ***
address 0x30, cause 'memory not mapped'
*** caught bus error ***
address 0x10186f5f7, cause 'non-existent physical address'
Traceback:
1: tryCatchOne(expr, names, parentenv, handlers[[1L]])
2: tryCatchList(expr, classes, parentenv, handlers)
3: tryCatch({ do.call(msg$data$fun, msg$data$args)}, error = function(e) { list(.error_worker_comm(e, "worker evaluation failed"))})
4: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
5: .recv_any(manager$backend)
6: .recv_any(manager$backend)
7: .manager_recv(manager)
8: .manager_recv(manager)
9: .collect_result(manager, reducer, progress, BPPARAM)
10: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length = length(redo_index))
11: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
12: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
13: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
14: bplapply(X = ddd, .wrapMapplyNotShared, .FUN = FUN, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
15: bplapply(X = ddd, .wrapMapplyNotShared, .FUN = FUN, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
16: bpmapply(.railMatChrRegionCov, sampleFiles, mappedPerXM, L, BPPARAM = BPPARAM.railChr, MoreArgs = list(chr = chr, regs = regions, verbose = verboseLoad))
17: bpmapply(.railMatChrRegionCov, sampleFiles, mappedPerXM, L, BPPARAM = BPPARAM.railChr, MoreArgs = list(chr = chr, regs = regions, verbose = verboseLoad))
18: FUN(X[[i]], ...)
19: lapply(regs_split, derfinder:::.railMatChrRegion, sampleFiles = sampleFiles, chr = chr, mappedPerXM = mappedPerXM, L = 1, verbose = verbose, BPPARAM.railChr = bpparam, verboseLoad = verboseLoad, chrlen = chrlen)
20: lapply(regs_split, derfinder:::.railMatChrRegion, sampleFiles = sampleFiles, chr = chr, mappedPerXM = mappedPerXM, L = 1, verbose = verbose, BPPARAM.railChr = bpparam, verboseLoad = verboseLoad, chrlen = chrlen)
21: coverage_matrix("SRP045638", "chr21", regions, chunksize = 2000, verboseLoad = FALSE, scale = FALSE)
22: eval(expr, envir, enclos)
23: eval(expr, envir, enclos)
24: eval_with_user_handlers(expr, envir, enclos, user_handlers)
25: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
26: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
27: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
28: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
29: 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, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
30: evaluate::evaluate(...)
31: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$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$render, options))
32: in_dir(input_dir(), expr)
33: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else 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)))
34: eng_r(options)
35: block_exec(params)
36: call_block(x)
37: process_group(group)
38: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
39: withCallingHandlers(expr, error = function(e) { loc = if (is.function(fun)) trimws(fun(label)) else "" if (loc != "") loc = sprintf(" at lines %s", loc) message(one_string(handler(e, loc)))})
40: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
41: process_file(text, output)
42: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
43: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
44: vweave_rmarkdown(...)
45: engine$weave(file, quiet = quiet, encoding = enc)
46: doTryCatch(return(expr), name, parentenv, handler)
47: tryCatchOne(expr, names, parentenv, handlers[[1L]])
48: tryCatchList(expr, classes, parentenv, handlers)
49: tryCatch({ engine$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)))})
50: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...