SANTA 2.24.0
Alex J. Cornish
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SANTA |
| Branch: RELEASE_3_10 |
| Last Commit: 24ff5f6 |
| Last Changed Date: 2019-10-29 13:08:37 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | [ ERROR ] | skipped | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SANTA
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* checking for file ‘SANTA/DESCRIPTION’ ... OK
* preparing ‘SANTA’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SANTA-vignette.Rmd’ using knitr
*** caught segfault ***
address 0x5500e4656e6d, cause 'memory not mapped'
Traceback:
1: do_read_bib(file, encoding = .Encoding, srcfile)
2: ReadBib(file, .Encoding = .Encoding, header = NULL, footer = NULL, check = check)
3: read.bibtex("refs.bib")
4: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
5: suppressMessages(bib <- read.bibtex("refs.bib"))
6: eval(expr, envir, enclos)
7: eval(expr, envir, enclos)
8: withVisible(eval(expr, envir, enclos))
9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
13: evaluate::evaluate(...)
14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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: knit(input, text = text, envir = envir, quiet = quiet)
23: knit2html(..., force_v1 = TRUE)
24: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
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) 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)))})
30: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)