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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 TitanCNA
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* checking for file ‘TitanCNA/DESCRIPTION’ ... OK
* preparing ‘TitanCNA’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 40097 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFYW23I/xshell9555329e057f' 2>&1
 ERROR
--- re-building ‘TitanCNA.Rnw’ using Sweave
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::setequal’ by ‘dplyr::setequal’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
Warning in fun(libname, pkgname) :
  Package 'TitanCNA' is deprecated and will be removed from Bioconductor
  version 3.23
titan: Loading data /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpFYW23I/Rinst95557ea62ed2/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpFYW23I/Rinst95557ea62ed2/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpFYW23I/Rinst95557ea62ed2/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpFYW23I/Rinst95557ea62ed2/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpFYW23I/Rinst95557ea62ed2/TitanCNA/extdata/test_tum_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading normal file:/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpFYW23I/Rinst95557ea62ed2/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpFYW23I/Rinst95557ea62ed2/TitanCNA/extdata/test_norm_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Warning in .replace_seqlevels_style(x_seqlevels, value) :
  found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one
Correcting Tumour
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Correcting Normal
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Normalizing Tumour by Normal
Removed Chrs: 
titan: Running HMM...
fwdBack: Iteration 1 chr: Warning: executing %dopar% sequentially: no parallel backend registered
1 
Using Coordinate Descent iteration 11 with Fval=-30217 and n=0.389 (map), s=[0.0079,0.3642], phi=1.472
fwdBack: loglik=-34137.4404
fwdBack: priorN=0.3549
fwdBack: priorS=-2.7329
fwdBack: priorVar=-433.6077
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2361
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34513.3185
fwdBack: Elapsed time for iteration 1: 0.0194m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26834 and n=0.2553 (map), s=[0.0068,0.4317], phi=1.473
fwdBack: loglik=-28578.8509
fwdBack: priorN=0.1318
fwdBack: priorS=-2.8160
fwdBack: priorVar=-748.8768
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2306
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29270.2988
fwdBack: Elapsed time for iteration 2: 0.0188m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26080 and n=0.2113 (map), s=[0.0068,0.4528], phi=1.489
fwdBack: loglik=-26355.2634
fwdBack: priorN=0.0000
fwdBack: priorS=-2.8127
fwdBack: priorVar=-818.5089
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1539
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27116.3952
fwdBack: Elapsed time for iteration 3: 0.0188m
fwdBack: Total elapsed time: 0.1006m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1 
 *** caught segfault ***
address 0x1, cause 'invalid permissions'

Traceback:
 1: eval(xpr, envir = envir)
 2: eval(xpr, envir = envir)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(eval(xpr, envir = envir), error = function(e) e)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch({    repeat {        args <- nextElem(it)        if (obj$verbose) {            cat(sprintf("evaluation # %d:\n", i))            print(args)        }        for (a in names(args)) assign(a, args[[a]], pos = envir,             inherits = FALSE)        r <- tryCatch(eval(xpr, envir = envir), error = function(e) e)        if (obj$verbose) {            cat("result of evaluating expression:\n")            print(r)        }        tryCatch(accumulator(list(r), i), error = function(e) {            cat("error calling combine function:\n")            print(e)            NULL        })        i <- i + 1    }}, error = function(e) {    if (!identical(conditionMessage(e), "StopIteration"))         stop(simpleError(conditionMessage(e), expr))})
11: e$fun(obj, substitute(ex), parent.frame(), e$data)
12: foreach(c = 1:numChrs, .combine = rbind, .noexport = c("data")) %dopar%     {        if (verbose == TRUE) {            message(c, " ", appendLF = FALSE)        }        .Call("fwd_backC_clonalCN", log(piGiZi[c, ]), py[, chrsI[[c]]],             gNoOUTStateParams$ct, gNoOUTStateParams$ZS, Z, posn[chrsI[[c]]],             txnZstrength * txnExpLen, txnExpLen, O)    }
13: runEMclonalCN(data, newParams, maxiter = 1, txnExpLen = convergeParams$txn_exp_len,     txnZstrength = convergeParams$txn_z_strength, useOutlierState = FALSE,     normalEstimateMethod = "fixed", estimateS = FALSE, estimatePloidy = F,     verbose = verbose)
14: removeEmptyClusters(data, convergeParams, outmat, proportionThreshold = proportionThreshold,     proportionThresholdClonal = proportionThresholdClonal, recomputeLogLik = recomputeLogLik,     verbose = verbose)
15: outputTitanResults(data, convergeParams, optimalPath, filename = NULL,     posteriorProbs = FALSE, subcloneProfiles = TRUE, correctResults = TRUE,     proportionThreshold = 0.05, proportionThresholdClonal = 0.05,     is.haplotypeData = FALSE)
16: eval(expr, .GlobalEnv)
17: eval(expr, .GlobalEnv)
18: withVisible(eval(expr, .GlobalEnv))
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: 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))})
23: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
24: evalFunc(ce, options)
25: tryCatchList(expr, classes, parentenv, handlers)
26: tryCatch(evalFunc(ce, options), finally = {    cat("\n")    sink()})
27: driver$runcode(drobj, chunk, chunkopts)
28: utils::Sweave(...)
29: engine$weave(file, quiet = quiet, encoding = enc)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: 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)))})
34: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...