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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data casper
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* checking for file ‘casper/DESCRIPTION’ ... OK
* preparing ‘casper’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 37459 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpNc4NBs/xshell843640487fe3' 2>&1
 ERROR
--- re-building ‘casper.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
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: GenomicRanges
Loading required package: GenomeInfoDb

 *** caught segfault ***
address 0xce, cause 'invalid permissions'

Traceback:
 1: calcKnownMultiple(exons = exons, exonwidth = exonwidth, transcripts = transcripts,     islandid = as.list(islandid), pc = pc, startcdf = startcdf,     lendis = lendis, lenvals = lenvals, readLength = readLength,     priorq = priorq, strand = strand, citype = citype, niter = niter,     burnin = burnin, verbose = verbose)
 2: f(islandid)
 3: .local(distrs, genomeDB, pc, readLength, islandid, rpkm, priorq,     priorqGeneExpr, citype, niter, burnin, mc.cores, verbose,     totReads)
 4: procExp(distrs, genomeDB, pc = pc@counts[[1]], readLength = readLength,     islandid = islandid, rpkm = rpkm, priorq = priorq, priorqGeneExpr = priorqGeneExpr,     niter = niter, burnin = burnin, mc.cores = mc.cores, citype = citype,     totReads = totReads)
 5: procExp(distrs, genomeDB, pc = pc@counts[[1]], readLength = readLength,     islandid = islandid, rpkm = rpkm, priorq = priorq, priorqGeneExpr = priorqGeneExpr,     niter = niter, burnin = burnin, mc.cores = mc.cores, citype = citype,     totReads = totReads)
 6: calcExp(distrs = distrs, genomeDB = hg19DB, pc = pc, readLength = 75,     rpkm = FALSE)
 7: eval(expr, .GlobalEnv)
 8: eval(expr, .GlobalEnv)
 9: withVisible(eval(expr, .GlobalEnv))
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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))})
14: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
15: evalFunc(ce, options)
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(evalFunc(ce, options), finally = {    cat("\n")    sink()})
18: driver$runcode(drobj, chunk, chunkopts)
19: utils::Sweave(...)
20: engine$weave(file, quiet = quiet, encoding = enc)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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)))})
25: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...