Error(s) in re-building vignettes:
sh: line 1: 22858 Segmentation fault      (core dumped) '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/Rtmp88FHKo/working_dir/RtmpdP6ALZ/file58e4453679e9' 2>&1 < '/tmp/Rtmp88FHKo/working_dir/RtmpdP6ALZ/file58e443d77a1b'
--- re-building ‘BioInstaller.Rmd’ using rmarkdown
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes


 *** caught segfault ***
address 0xc800010009, cause 'memory not mapped'

Traceback:
 1: git2r::clone(github_url, destdir)
 2: git.download(name, download.dir, version, github_url, use_git2r,     recursive_clone, verbose)
 3: install.github(name = i, destdir = destdir[count], download.dir = download.dir[count],     github.cfg = github.cfg, name.saved = name.saved[count],     version = version[count], local.source = local.source[count],     show.all.versions = show.all.versions, db = db, download.only = download.only,     verbose = verbose, showWarnings = showWarnings, dependence.need = dependence.need,     extra.list = extra.list, rmcd.parse = rcmd.parse, bash.parse = bash.parse,     glue.parse = glue.parse, glue.flag = glue.flag, save.to.db = save.to.db,     overwrite = overwrite, ...)
 4: install.bioinfo("github_demo", download.dir = download.dir, download.only = TRUE,     verbose = FALSE)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: tryCatch({    install.bioinfo("github_demo", download.dir = download.dir,         download.only = TRUE, verbose = FALSE)    install.bioinfo("github_demo", local.source = download.dir)}, error = function(e) {    message("Please check the SSL or connection with GitHub")})
 9: eval(expr, envir, enclos)
10: eval(expr, envir, enclos)
11: withVisible(eval(expr, envir, enclos))
12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
16: evaluate::evaluate(...)
17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
18: 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$render, options)))
19: block_exec(params)
20: call_block(x)
21: process_group.block(group)
22: process_group(group)
23: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
33: tools:::.buildOneVignette("BioInstaller.Rmd", "/data/gannet/ripley/R/packages/tests-clang/BioInstaller.Rcheck/vign_test/BioInstaller",     TRUE, FALSE, "BioInstaller", "UTF-8", "/tmp/Rtmp88FHKo/working_dir/RtmpdP6ALZ/file58e45c8befaa.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘download.Rmd’ using rmarkdown
--- finished re-building ‘download.Rmd’

--- re-building ‘items_description.Rmd’ using rmarkdown
--- finished re-building ‘items_description.Rmd’

--- re-building ‘plugins_of_BioInstaller_shiny.Rmd’ using rmarkdown
--- finished re-building ‘plugins_of_BioInstaller_shiny.Rmd’

--- re-building ‘start_shiny_of_BioInstaller.Rmd’ using rmarkdown
--- finished re-building ‘start_shiny_of_BioInstaller.Rmd’

--- re-building ‘write_configuration_file.Rmd’ using rmarkdown
--- finished re-building ‘write_configuration_file.Rmd’

SUMMARY: processing the following file failed:
  ‘BioInstaller.Rmd’

Error: Vignette re-building failed.
Execution halted