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). 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 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 [[alternative HTML version deleted]]
>>>>> 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.> RobertTo 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
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 >