From goran.brostrom at umu.se  Wed Dec  6 17:14:23 2017
From: goran.brostrom at umu.se (=?UTF-8?Q?G=c3=b6ran_Brostr=c3=b6m?=)
Date: Wed, 6 Dec 2017 17:14:23 +0100
Subject: [Rd] FW: R-devel error
In-Reply-To: <23079.50835.483974.112384@stat.math.ethz.ch>
References: <BY2PR09MB0293D6F3EDCE2DF3EFC57403EC3D0@BY2PR09MB0293.namprd09.prod.outlook.com>
 <23079.50835.483974.112384@stat.math.ethz.ch>
Message-ID: <e6fd7a97-fe04-80fa-f667-261e721b66c1@umu.se>

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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] FW: R-devel error
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