Fantastic! Thank you. Ben
> Le 1 janv. 2020 à 20:38, Martin Morgan <mtmorgan.b...@gmail.com> a écrit : > > This is from the bibtex package > > https://github.com/romainfrancois/bibtex/issues/23 > > And the solution is to either not use that package (settling for base R > functionality) or wait for the upstream fix. > > Martin > > > On 1/2/20, 7:06 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay" > <bioc-devel-boun...@r-project.org on behalf of > benjamin.tremb...@uwaterloo.ca> wrote: > > Dear bioc-devel, > > My package has been getting a strange error on merida1 (also celaya2) > during the initial install phase. I've pasted it at the bottom of this > message. > > My question is: what can I do to figure out what the problem is? I already > work > on a Mac currently, and R CMD check runs fine. I've also recently patched > the > package, but that was for a different error -- the one in question was also > occurring for the previous version, which used to pass without issues. I’ve > downloaded the bioconductor_full docker image to try and replicate the test > environment, but that went fine too. Perhaps it's OS/hardware specific? (I > use > macOS Catalina). > > Any help would be greatly appreciated. My package is over at: > http://bioconductor.org/packages/release/bioc/html/universalmotif.html > > Thank you, > > Ben T > > The error in question. Something appears to go wrong when processing the > Rd files. > > ** help > > *** caught segfault *** > address 0x0, cause 'memory not mapped' > > Traceback: > 1: doTryCatch(return(expr), name, parentenv, handler) > 2: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 3: tryCatchList(expr, classes, parentenv, handlers) > 4: tryCatch(.External("do_read_bib", file = file, encoding = encoding, > srcfile = srcfile), error = function(e) { if (!any(grepl("unprotect_ptr", > e))) stop(geterrmessage(), call. = FALSE) else stop("Invalid bib > file", call. = FALSE)}) > 5: withCallingHandlers(tryCatch(.External("do_read_bib", file = file, > encoding = encoding, srcfile = srcfile), error = function(e) { if > (!any(grepl("unprotect_ptr", e))) stop(geterrmessage(), call. = > FALSE) else stop("Invalid bib file", call. = FALSE)}), warning = > function(w) { if (any(grepl("syntax error, unexpected [$]end", w))) > invokeRestart("muffleWarning")}) > 6: read.bib(file = fn, encoding = encoding) > 7: get_bibentries(package = package, ..., stop_on_error = FALSE) > 8: Rdpack::insert_citeOnly(key = "euclidean", package = "universalmotif", > cached_env = .Rdpack.currefs) > 9: eval(expr, env) > 10: eval(expr, env) > 11: withVisible(eval(expr, env)) > 12: doTryCatch(return(expr), name, parentenv, handler) > 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 14: tryCatchList(expr, classes, parentenv, handlers) > 15: tryCatch(withVisible(eval(expr, env)), error = function(e) e) > 16: evalWithOpt(ce, options, env) > 17: processRdChunk(block, stage, options, env, macros = macros) > 18: recurse(block[[i]]) > 19: recurse(block[[i]]) > 20: recurse(block[[i]]) > 21: recurse(block) > 22: getDynamicFlags(block) > 23: recurse(block) > 24: expandDynamicFlags(recurse(block), options) > 25: processRdSexprs(Rd, "build", options, macros = attr(Rd, "macros")) > 26: prepare_Rd(f, encoding = encoding, defines = os, stages = stages, > warningCalls = FALSE, stage2 = step > 1L, stage3 = step > 2L, macros > = macros) > 27: FUN(X[[i]], ...) > 28: lapply(files, .fetch_Rd_object) > 29: .build_Rd_db(dir, manfiles, db_file = db_file, encoding = encoding, > built_file = built_file) > 30: .install_package_Rd_objects(".", instdir, encoding) > 31: doTryCatch(return(expr), name, parentenv, handler) > 32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 33: tryCatchList(expr, classes, parentenv, handlers) > 34: tryCatch(expr, error = function(e) { call <- conditionCall(e) if > (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) > call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix > <- paste("Error in", dcall, ": ") LONG <- 75L sm <- > strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type > = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L > + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") > if (w > LONG) prefix <- paste0(prefix, "\n ") } else > prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") > .Internal(seterrmessage(msg[1L])) if (!silent && > isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) > .Internal(printDeferredWarnings()) } invisible(structure(msg, > class = "try-error", condition = e))}) > 35: try(.install_package_Rd_objects(".", instdir, encoding)) > 36: do_install_source(pkg_name, instdir, pkg, desc) > 37: do_install(pkg) > 38: tools:::.install_packages() > An irrecoverable exception occurred. R is aborting now ... > /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 14976 Done > echo 'tools:::.install_packages()' > 14977 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C > "${R_HOME}/bin/R" $myArgs --slave --args ${args} > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
