Pearce, Robert <pearce.rob...@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@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$weave(file, quiet = quiet, encoding = enc)
setwd(startdir) find_vignette_product(name, by = "weave", engine =
engine)}, error = function(e) { stop(gettextf("processing vignette '%s'
failed with diagnostics:\n%s", file, conditionMessage(e)), domain =
NA, call. = FALSE)})
17: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
[nfslocal@lynne tmp]$
-----------------------------------------------------------
-------------
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@r-project.org' <r-devel@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
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