############################################################################## ############################################################################## ### ### 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/Rtmp5D63ce/Rinstb7fbd4ff7f92b/TitanCNA/extdata/test_alleleCounts_chr2.txt Reading GC and mappability files Slurping: /tmp/Rtmp5D63ce/Rinstb7fbd4ff7f92b/TitanCNA/extdata/gc_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Slurping: /tmp/Rtmp5D63ce/Rinstb7fbd4ff7f92b/TitanCNA/extdata/map_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Loading tumour file:/tmp/Rtmp5D63ce/Rinstb7fbd4ff7f92b/TitanCNA/extdata/test_tum_chr2.wig Slurping: /tmp/Rtmp5D63ce/Rinstb7fbd4ff7f92b/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/Rtmp5D63ce/Rinstb7fbd4ff7f92b/TitanCNA/extdata/test_norm_chr2.wig Slurping: /tmp/Rtmp5D63ce/Rinstb7fbd4ff7f92b/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=-30482 and n=0.3984 (map), s=[0.0083,0.3768], phi=1.502 fwdBack: loglik=-34145.6788 fwdBack: priorN=0.3633 fwdBack: priorS=-2.6666 fwdBack: priorVar=-439.1894 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.0921 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 1 complete loglik=-34526.9201 fwdBack: Elapsed time for iteration 1: 0.0426m fwdBack: Iteration 2 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26818 and n=0.2536 (map), s=[0.0091,0.4330], phi=1.469 fwdBack: loglik=-28968.4983 fwdBack: priorN=0.1273 fwdBack: priorS=-2.5344 fwdBack: priorVar=-752.4092 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.2552 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 2 complete loglik=-29663.2261 fwdBack: Elapsed time for iteration 2: 0.0419m fwdBack: Iteration 3 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26058 and n=0.2115 (map), s=[0.0069,0.4527], phi=1.483 fwdBack: loglik=-26330.0516 fwdBack: priorN=0.0006 fwdBack: priorS=-2.7979 fwdBack: priorVar=-822.9313 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.1817 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 3 complete loglik=-27095.6183 fwdBack: Elapsed time for iteration 3: 0.0415m fwdBack: Total elapsed time: 0.2088m 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)