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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: 75205 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpoAu8FB/xshell10c214257a3fe' 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/tmp/RtmpoAu8FB/Rinst10c215b1a8180/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: /private/tmp/RtmpoAu8FB/Rinst10c215b1a8180/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /private/tmp/RtmpoAu8FB/Rinst10c215b1a8180/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:/private/tmp/RtmpoAu8FB/Rinst10c215b1a8180/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /private/tmp/RtmpoAu8FB/Rinst10c215b1a8180/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/tmp/RtmpoAu8FB/Rinst10c215b1a8180/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /private/tmp/RtmpoAu8FB/Rinst10c215b1a8180/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=-30510 and n=0.3981 (map), s=[0.0083,0.3771], phi=1.503
fwdBack: loglik=-34158.7683
fwdBack: priorN=0.3631
fwdBack: priorS=-2.6654
fwdBack: priorVar=-434.4538
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0879
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34535.2687
fwdBack: Elapsed time for iteration 1: 0.0730m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26863 and n=0.2534 (map), s=[0.0091,0.4333], phi=1.469
fwdBack: loglik=-29014.2395
fwdBack: priorN=0.1268
fwdBack: priorS=-2.5290
fwdBack: priorVar=-743.4698
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2534
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29700.0212
fwdBack: Elapsed time for iteration 2: 0.0754m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26112 and n=0.2116 (map), s=[0.0069,0.4527], phi=1.483
fwdBack: loglik=-26389.2429
fwdBack: priorN=0.0009
fwdBack: priorS=-2.7924
fwdBack: priorVar=-811.7070
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1811
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27143.5788
fwdBack: Elapsed time for iteration 3: 0.0707m
fwdBack: Total elapsed time: 0.3799m
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 ...