[Rd] FW: R-devel error
Göran Broström
goran.brostrom at umu.se
Wed Dec 6 17:14:23 CET 2017
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.
Göran Broström
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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
More information about the R-devel
mailing list