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### Running command:
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###   /home/biocbuild/R/R/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 ... 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 ‘GenomeInfoDb::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’
titan: Loading data /home/biocbuild/tmp/RtmpdiKRUw/Rinst11f7a467bad992/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: /home/biocbuild/tmp/RtmpdiKRUw/Rinst11f7a467bad992/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /home/biocbuild/tmp/RtmpdiKRUw/Rinst11f7a467bad992/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:/home/biocbuild/tmp/RtmpdiKRUw/Rinst11f7a467bad992/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /home/biocbuild/tmp/RtmpdiKRUw/Rinst11f7a467bad992/TitanCNA/extdata/test_tum_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading normal file:/home/biocbuild/tmp/RtmpdiKRUw/Rinst11f7a467bad992/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /home/biocbuild/tmp/RtmpdiKRUw/Rinst11f7a467bad992/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=-30484 and n=0.3979 (map), s=[0.0083,0.3768], phi=1.502
fwdBack: loglik=-34150.9778
fwdBack: priorN=0.3629
fwdBack: priorS=-2.6684
fwdBack: priorVar=-437.1514
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0914
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34530.1824
fwdBack: Elapsed time for iteration 1: 0.0488m
fwdBack: Iteration 2 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26830 and n=0.2536 (map), s=[0.009,0.433], phi=1.47
fwdBack: loglik=-28963.0922
fwdBack: priorN=0.1273
fwdBack: priorS=-2.5437
fwdBack: priorVar=-749.7719
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2503
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29655.1871
fwdBack: Elapsed time for iteration 2: 0.0485m
fwdBack: Iteration 3 chr: 1 
Using Coordinate Descent iteration 11 with Fval=-26077 and n=0.2115 (map), s=[0.0069,0.4527], phi=1.484
fwdBack: loglik=-26349.6827
fwdBack: priorN=0.0005
fwdBack: priorS=-2.7968
fwdBack: priorVar=-818.9294
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1772
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27111.2419
fwdBack: Elapsed time for iteration 3: 0.0479m
fwdBack: Total elapsed time: 0.2268m
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1 
 *** caught segfault ***
address 0x1, cause 'memory not mapped'

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 ...