############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 TitanCNA ### ############################################################################## ############################################################################## * 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/RtmpBSlOQJ/Rinst26e536d3c7470/TitanCNA/extdata/test_alleleCounts_chr2.txt Reading GC and mappability files Slurping: /tmp/RtmpBSlOQJ/Rinst26e536d3c7470/TitanCNA/extdata/gc_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Slurping: /tmp/RtmpBSlOQJ/Rinst26e536d3c7470/TitanCNA/extdata/map_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Loading tumour file:/tmp/RtmpBSlOQJ/Rinst26e536d3c7470/TitanCNA/extdata/test_tum_chr2.wig Slurping: /tmp/RtmpBSlOQJ/Rinst26e536d3c7470/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/RtmpBSlOQJ/Rinst26e536d3c7470/TitanCNA/extdata/test_norm_chr2.wig Slurping: /tmp/RtmpBSlOQJ/Rinst26e536d3c7470/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=-30504 and n=0.3984 (map), s=[0.0083,0.3770], phi=1.501 fwdBack: loglik=-34155.0443 fwdBack: priorN=0.3633 fwdBack: priorS=-2.6651 fwdBack: priorVar=-435.7137 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.0952 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 1 complete loglik=-34532.8113 fwdBack: Elapsed time for iteration 1: 0.0416m fwdBack: Iteration 2 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26854 and n=0.2537 (map), s=[0.0092,0.4330], phi=1.467 fwdBack: loglik=-29008.2787 fwdBack: priorN=0.1275 fwdBack: priorS=-2.5233 fwdBack: priorVar=-745.2204 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.2624 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 2 complete loglik=-29695.8138 fwdBack: Elapsed time for iteration 2: 0.0429m fwdBack: Iteration 3 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26099 and n=0.2117 (map), s=[0.0069,0.4526], phi=1.482 fwdBack: loglik=-26376.0354 fwdBack: priorN=0.0013 fwdBack: priorS=-2.7957 fwdBack: priorVar=-814.0993 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.1886 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 3 complete loglik=-27132.7741 fwdBack: Elapsed time for iteration 3: 0.0415m fwdBack: Total elapsed time: 0.2102m 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)