Error(s) in re-building vignettes:
--- re-building ‘BIRDS.Rmd’ using rmarkdown
--- finished re-building ‘BIRDS.Rmd’

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

sh: line 1: 3806316 Segmentation fault      (core dumped) R_LIBS=/tmp/RtmpJNaaDX/RLIBS_382e8337e78070 R_ENVIRON_USER='' R_LIBS_USER='' R_LIBS_SITE='no_such_dir' '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/RtmpJNaaDX/working_dir/RtmpQUosnL/file398f073d6e39b5' 2>&1 < '/tmp/RtmpJNaaDX/working_dir/RtmpQUosnL/file398f075951016c'
Warning: elapsed-time limit of 30 minutes reached for sub-process
--- re-building ‘working_with_xts_timeseries.Rmd’ using rmarkdown
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded datum WGS_1984 in Proj4 definition
Warning in spTransform(polygon, CRSobj = CRS("+init=epsg:3857")) :
  NULL source CRS comment, falling back to PROJ string
Warning in spTransform(polygon, CRSobj = CRS("+init=epsg:3857")) :
  +init dropped in PROJ string
Warning in wkt(obj) : CRS object has no comment
Warning in proj4string(obj) :
  CRS object has comment, which is lost in output

Quitting from lines 26-43 (working_with_xts_timeseries.Rmd) 

 *** caught segfault ***
address 0x44c6, cause 'memory not mapped'

Traceback:
 1: dev.off(dv)
 2: block_exec(params)
 3: call_block(x)
 4: process_group.block(group)
 5: process_group(group)
 6: 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$get("infile"),             ") ")    })
 7: process_file(text, output)
 8: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 9: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
10: vweave_rmarkdown(...)
11: engine$weave(file, quiet = quiet, encoding = enc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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)))})
16: tools:::.buildOneVignette("working_with_xts_timeseries.Rmd",     "/data/gannet/ripley/R/packages/tests-clang/BIRDS.Rcheck/vign_test/BIRDS",     TRUE, FALSE, "working_with_xts_timeseries", "UTF-8", "/tmp/RtmpJNaaDX/working_dir/RtmpQUosnL/file398f07526f457e.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following file failed:
  ‘working_with_xts_timeseries.Rmd’

Error: Vignette re-building failed.
Execution halted