############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rGADEM ### ############################################################################## ############################################################################## * checking for file ‘rGADEM/DESCRIPTION’ ... OK * preparing ‘rGADEM’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ...sh: line 1: 42015 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpSlaFpU/xshell988f59bad250' 2>&1 ERROR --- re-building ‘rGADEM.Rnw’ using Sweave Loading required package: Biostrings Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: BSgenome Loading required package: GenomicRanges Loading required package: BiocIO Loading required package: rtracklayer Attaching package: ‘rtracklayer’ The following object is masked from ‘package:BiocIO’: FileForFormat Loading required package: seqLogo Loading required package: grid Attaching package: ‘grid’ The following object is masked from ‘package:Biostrings’: pattern Attaching package: ‘rGADEM’ The following object is masked from ‘package:seqLogo’: consensus *** caught segfault *** address 0x8, cause 'invalid permissions' Traceback: 1: GADEM(Sequences, verbose = 1, genome = Hsapiens) 2: eval(expr, .GlobalEnv) 3: eval(expr, .GlobalEnv) 4: withVisible(eval(expr, .GlobalEnv)) 5: doTryCatch(return(expr), name, parentenv, handler) 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 8: 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, nlines = 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))}) 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE) 10: evalFunc(ce, options) 11: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()}) 13: driver$runcode(drobj, chunk, chunkopts) 14: utils::Sweave(...) 15: engine$weave(file, quiet = quiet, encoding = enc) 16: doTryCatch(return(expr), name, parentenv, handler) 17: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 18: tryCatchList(expr, classes, parentenv, handlers) 19: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 20: tools::buildVignettes(dir = ".", tangle = TRUE) An irrecoverable exception occurred. R is aborting now ...