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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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 ‘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 /tmp/RtmpJ8Vwbk/Rinst3daa3b579d1225/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: /tmp/RtmpJ8Vwbk/Rinst3daa3b579d1225/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /tmp/RtmpJ8Vwbk/Rinst3daa3b579d1225/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:/tmp/RtmpJ8Vwbk/Rinst3daa3b579d1225/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /tmp/RtmpJ8Vwbk/Rinst3daa3b579d1225/TitanCNA/extdata/test_tum_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading normal file:/tmp/RtmpJ8Vwbk/Rinst3daa3b579d1225/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /tmp/RtmpJ8Vwbk/Rinst3daa3b579d1225/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=-30488 and n=0.3982 (map), s=[0.0083,0.3765], phi=1.503
fwdBack: loglik=-34147.9451
fwdBack: priorN=0.3631
fwdBack: priorS=-2.6672
fwdBack: priorVar=-436.8401
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0892
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34526.8348
fwdBack: Elapsed time for iteration 1: 0.0428m
fwdBack: Iteration 2 chr: 1
Using Coordinate Descent iteration 11 with Fval=-26840 and n=0.2538 (map), s=[0.009,0.433], phi=1.469
fwdBack: loglik=-28978.4901
fwdBack: priorN=0.1277
fwdBack: priorS=-2.5380
fwdBack: priorVar=-748.0230
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2512
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29668.8310
fwdBack: Elapsed time for iteration 2: 0.0445m
fwdBack: Iteration 3 chr: 1
Using Coordinate Descent iteration 11 with Fval=-26082 and n=0.2115 (map), s=[0.0069,0.4528], phi=1.484
fwdBack: loglik=-26358.5358
fwdBack: priorN=0.0008
fwdBack: priorS=-2.7969
fwdBack: priorVar=-817.5758
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1778
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27118.7419
fwdBack: Elapsed time for iteration 3: 0.0418m
fwdBack: Total elapsed time: 0.2168m
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 ...
Segmentation fault (core dumped)