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 >
Robert, To expand a bit on Goran's point, is it possible that you have an old library with packages installed that your R-devel is hitting. The R headers changes relatively recently, so any packages with compiled code that were built long enough ago (I don't have the exact date off the top of my head) need to be rebuilt before they can be safely used. If this is happening in a state where both the package in question AND all it's dependencies are freshly built under the exact version of R-devel you're trying to check httk with, then the above isn't the problem and something else must be going on. Best, ~G On Wed, Dec 6, 2017 at 8:14 AM, G?ran Brostr?m <goran.brostrom at umu.se> wrote:> 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 >> >> > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Gabriel Becker, PhD Scientist (Bioinformatics) Genentech Research [[alternative HTML version deleted]]
library() in R-devel checks that packages are built for the current ABI and signals an error if they are not. A segfault is likely a pre-existing bug unmasked by the changed memory layout. Several of these have been resolved by recent package updates. I also cannot reproduce the problem on current R-devel with fairly current packages from CRAN. Best, luke On Wed, 6 Dec 2017, Gabriel Becker wrote:> Robert, > > To expand a bit on Goran's point, is it possible that you have an old > library with packages installed that your R-devel is hitting. The R headers > changes relatively recently, so any packages with compiled code that were > built long enough ago (I don't have the exact date off the top of my head) > need to be rebuilt before they can be safely used. > > If this is happening in a state where both the package in question AND all > it's dependencies are freshly built under the exact version of R-devel > you're trying to check httk with, then the above isn't the problem and > something else must be going on. > > Best, > ~G > > On Wed, Dec 6, 2017 at 8:14 AM, G?ran Brostr?m <goran.brostrom at umu.se> > wrote: > >> 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 >>> >>> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > > -- > Gabriel Becker, PhD > Scientist (Bioinformatics) > Genentech Research > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tierney at uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu