##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TitanCNA
###
##############################################################################
##############################################################################
* 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: 87787 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpJ7bFRd/xshell1437a135fe2b6' 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/RtmpJ7bFRd/Rinst1437a70d2694d/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: /private/tmp/RtmpJ7bFRd/Rinst1437a70d2694d/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /private/tmp/RtmpJ7bFRd/Rinst1437a70d2694d/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/RtmpJ7bFRd/Rinst1437a70d2694d/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /private/tmp/RtmpJ7bFRd/Rinst1437a70d2694d/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/RtmpJ7bFRd/Rinst1437a70d2694d/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /private/tmp/RtmpJ7bFRd/Rinst1437a70d2694d/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=-30483 and n=0.3982 (map), s=[0.0083,0.3771], phi=1.501
fwdBack: loglik=-34149.1510
fwdBack: priorN=0.3631
fwdBack: priorS=-2.6669
fwdBack: priorVar=-438.5193
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.0950
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34529.7255
fwdBack: Elapsed time for iteration 1: 0.0566m
fwdBack: Iteration 2 chr: 1
Using Coordinate Descent iteration 11 with Fval=-26821 and n=0.2536 (map), s=[0.0091,0.4331], phi=1.468
fwdBack: loglik=-28968.1418
fwdBack: priorN=0.1272
fwdBack: priorS=-2.5344
fwdBack: priorVar=-751.7263
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2577
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29662.1894
fwdBack: Elapsed time for iteration 2: 0.0394m
fwdBack: Iteration 3 chr: 1
Using Coordinate Descent iteration 11 with Fval=-26063 and n=0.2114 (map), s=[0.0069,0.4529], phi=1.483
fwdBack: loglik=-26335.0772
fwdBack: priorN=0.0001
fwdBack: priorS=-2.7987
fwdBack: priorVar=-821.8655
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1838
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27099.5815
fwdBack: Elapsed time for iteration 3: 0.0514m
fwdBack: Total elapsed time: 0.2299m
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 ...