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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/RtmphpUalU/Rinst3140cb573e274a/TitanCNA/extdata/test_alleleCounts_chr2.txt
Reading GC and mappability files
Slurping: /tmp/RtmphpUalU/Rinst3140cb573e274a/TitanCNA/extdata/gc_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Slurping: /tmp/RtmphpUalU/Rinst3140cb573e274a/TitanCNA/extdata/map_chr2.wig
Parsing: fixedStep chrom=2 start=1 step=1000 span=1000
Sorting by decreasing chromosome size
Loading tumour file:/tmp/RtmphpUalU/Rinst3140cb573e274a/TitanCNA/extdata/test_tum_chr2.wig
Slurping: /tmp/RtmphpUalU/Rinst3140cb573e274a/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/RtmphpUalU/Rinst3140cb573e274a/TitanCNA/extdata/test_norm_chr2.wig
Slurping: /tmp/RtmphpUalU/Rinst3140cb573e274a/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=-30289 and n=0.3909 (map), s=[0.008,0.367], phi=1.48
fwdBack: loglik=-34142.8114
fwdBack: priorN=0.3567
fwdBack: priorS=-2.7177
fwdBack: priorVar=-433.3041
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2002
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34518.3331
fwdBack: Elapsed time for iteration 1: 0.0428m
fwdBack: Iteration 2 chr: 1
Using Coordinate Descent iteration 11 with Fval=-26843 and n=0.2551 (map), s=[0.0071,0.4319], phi=1.473
fwdBack: loglik=-28664.3011
fwdBack: priorN=0.1311
fwdBack: priorS=-2.7753
fwdBack: priorVar=-747.2140
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.2336
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 2 complete loglik=-29354.0493
fwdBack: Elapsed time for iteration 2: 0.0436m
fwdBack: Iteration 3 chr: 1
Using Coordinate Descent iteration 11 with Fval=-26091 and n=0.2114 (map), s=[0.0068,0.4528], phi=1.488
fwdBack: loglik=-26365.6341
fwdBack: priorN=0.0003
fwdBack: priorS=-2.8097
fwdBack: priorVar=-816.0498
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=-1.1576
fwdBack: priorPiG=60.3628
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 3 complete loglik=-27124.3073
fwdBack: Elapsed time for iteration 3: 0.0430m
fwdBack: Total elapsed time: 0.2147m
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)