Error in re-building vignettes:
  ...
Loading required package: ape
No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Struthioniformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Tinamiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Craciformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Galliformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Anseriformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Turniciformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Piciformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Galbuliformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Bucerotiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Upupiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Trogoniformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Coraciiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Coliiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Cuculiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Psittaciformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Apodiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Trochiliformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Musophagiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Strigiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Columbiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Gruiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Ciconiiformes'

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Passeriformes'


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Allenopithecus_nigroviridis'


 *** caught segfault ***
address 0x249, cause 'memory not mapped'

Traceback:
 1: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
 2: crul_fetch(opts)
 3: private$make_request(rr)
 4: cli$get(sprintf("entrez/eutils/%s.fcgi", path), query = tc(query))
 5: repeat_until_it_works(try_again_errors, "esearch", query = query_args,     ...)
 6: FUN(X[[i]], ...)
 7: lapply(pieces, .fun, ...)
 8: structure(lapply(pieces, .fun, ...), dim = dim(pieces))
 9: llply(.data = .data, .fun = .fun, ..., .progress = .progress,     .inform = .inform, .parallel = .parallel, .paropts = .paropts)
10: ldply(sciname, fun, ask, messages, rows, ...)
11: get_uid(nexml@otus[[j]]@otu[[i]]@label)
12: taxize_nexml(.)
13: function_list[[k]](value)
14: withVisible(function_list[[k]](value))
15: freduce(value, `_function_list`)
16: `_fseq`(`_lhs`)
17: eval(quote(`_fseq`(`_lhs`)), env, env)
18: eval(quote(`_fseq`(`_lhs`)), env, env)
19: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
20: add_trees(primates$phy) %>% add_characters(primates$dat, ., append = TRUE) %>%     taxize_nexml()
21: eval(expr, envir, enclos)
22: eval(expr, envir, enclos)
23: withVisible(eval(expr, envir, enclos))
24: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
25: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
26: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
27: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&         options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
30: 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$render, options)))
31: block_exec(params)
32: call_block(x)
33: process_group.block(group)
34: process_group(group)
35: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
36: process_file(text, output)
37: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,     encoding = encoding)
38: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv())
39: vweave_rmarkdown(...)
40: engine$weave(file, quiet = quiet, encoding = enc)
41: doTryCatch(return(expr), name, parentenv, handler)
42: tryCatchOne(expr, names, parentenv, handlers[[1L]])
43: tryCatchList(expr, classes, parentenv, handlers)
44: tryCatch({    engine$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)})
45: buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RNeXML.Rcheck/vign_test/RNeXML")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault