R-devel error

Interesting, yesterday I had exactly this problem, but today I solved it
(see the R-pkg-devel list) by _installing_ R-devel and

update.packages(checkBuilt = TRUE)

I also tried it on Martin's Fedora 26 example below. Worked fine (had to
install some packages...)

On ubuntu 16.04.

G?ran Brostr?m


On 2017-12-06 11:29, Martin Maechler wrote:

Pearce, Robert <Pearce.Robert at epa.gov>

     on Tue, 5 Dec 2017 21:31:09 +0000 writes:

     > I am resubmitting this bug report but with additional information.

I am running this with windows 10:  w64-mingw32 with R Under development
(unstable) (2017-12-04 r73829).

There is no such message (as you cite below) in the R-devel archives:
       https://stat.ethz.ch/pipermail/r-devel/2017-November/thread.html

Hence it was never posted for some reason
(You may have *sent* it, but it never arrived "safely")

     > I build 'httk' from the command prompt using 'R CMD build httk'

after installing the required packages. Then when the vignettes are being
created, it crashes. Today I installed the latest versions of Rtools,
MikTex and R-devel and still got the same error. We have also replicated
this on another machine. I am able to successfully build the package in
this way with R 3.4.3.

Robert

To make this reproducible, indeed, I also get
problem, possibly the same as you on my Linux machine (Fedora 26):

1. Get  httk_1.7.tar.gz from https://cran.r-project.org/package=httk

2. unpack (for me:)
        tar xf httk_1.7.tar.gz
3.
        R-devel CMD build httk

I get the following.
Notably after having waited several minutes at the prompt
(line  of output):

  '* creating vignettes '

   -----------------------------------------------------------
-------------
   [nfslocal at lynne tmp]$ R-devel CMD build httk
   * checking for file ?httk/DESCRIPTION? ... OK
   * preparing ?httk?:
   * checking DESCRIPTION meta-information ... OK
   * cleaning src
   * installing the package to process help pages
   * saving partial Rd database
   * creating vignettes ...sh: line 1: 16259 Segmentation fault
(core dumped) '/u/maechler/R/D/r-devel/inst/bin/Rscript' --vanilla
--default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" >
'/tmp/RtmpV1grVw/xshell3e793c7d5258' 2>&1
    ERROR

    *** caught segfault ***
   address 0x1, cause 'memory not mapped'

   Traceback:
    1: .Call(C_stri_locate_all_regex, str, pattern, omit_no_match,
opts_regex)
    2: stri_locate_all_regex(string, pattern, omit_no_match = TRUE,
 opts_regex = opts)
    3: stringr::str_locate_all(input, inline.code)
    4: parse_inline(g, patterns)
    5: FUN(X[[i]], ...)
    6: lapply(groups, function(g) {    block = grepl(chunk.begin, g[1])
  if (!set.preamble && !parent_mode()) {        return(if (block) "" else
g)    }    if (block) {        n = length(g)        if (n >= 2 &&
grepl(chunk.end, g[n]))             g = g[-n]        g = strip_block(g,
patterns$chunk.code)        params.src = if (group_pattern(chunk.begin)) {
          stringr::str_trim(gsub(chunk.begin, "\\1", g[1]))        }
    else ""        parse_block(g[-1], g[1], params.src)    }    else
parse_inline(g, patterns)})
    7: split_file(lines = text)
    8: process_file(text, output)
    9: knitr::knit(knit_input, knit_output, envir = envir, quiet =
quiet,     encoding = encoding)
   10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir
= globalenv())
   11: vweave_rmarkdown(...)
   12: engine$weave(file, quiet = quiet, encoding = enc)
   13: doTryCatch(return(expr), name, parentenv, handler)
   14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   15: tryCatchList(expr, classes, parentenv, handlers)
   16: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)    find_vignette_product(name, by = "weave", engine =
engine)}, error = function(e) {    stop(gettextf("processing vignette '%s'
failed with diagnostics:\n%s",         file, conditionMessage(e)), domain =
NA, call. = FALSE)})
   17: tools::buildVignettes(dir = ".", tangle = TRUE)
   An irrecoverable exception occurred. R is aborting now ...
   [nfslocal at lynne tmp]$
   -----------------------------------------------------------
-------------


I've seen this (segfault, triggered from stringr stuff) before,
occasionally and always thought it was a consequence of a messup
(different R versions and package installations in libraries I
use on the same computer....),  but now I have convinced myself
that this is not the case: I can easily reproduce the above using

        tools::buildVignettes(dir = "<mypath_to>/httk")

==> So I'd suggest there's a pretty low-level bug somewhere.

- Either in 'stringr' or 'stringi' in their C code using
   things they should not (because not in R's API),
   which now shows in R-devel where many "inner workings" have been
   modified (key "ALTREP")

- or in R-devel .. in these new "inner workings".


I don't have time to dig further at the moment.

Thank you, Robert, for your report!

Martin Maechler,
ETH Zurich

     > From: Pearce, Robert
     > Sent: Monday, November 20, 2017 11:32 AM
     > To: 'r-devel at r-project.org' <r-devel at r-project.org>
     > Subject: R-devel error

     > Hello,

     > During the last week I've been getting an error with r-devel when

building the source package for 'httk'. Everything works fine until:
'creating vignettes...' . Then I get a pop-up stating: 'R for Windows
front-end has stopped working... close the program'. I have installed the
latest version of R, and this error does not occur.

     > Robert Pearce