############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/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 ... 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 ‘GenomeInfoDb::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’ titan: Loading data /tmp/RtmpR2YV3E/Rinst3f48ec3c4ae151/TitanCNA/extdata/test_alleleCounts_chr2.txt Reading GC and mappability files Slurping: /tmp/RtmpR2YV3E/Rinst3f48ec3c4ae151/TitanCNA/extdata/gc_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Slurping: /tmp/RtmpR2YV3E/Rinst3f48ec3c4ae151/TitanCNA/extdata/map_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Loading tumour file:/tmp/RtmpR2YV3E/Rinst3f48ec3c4ae151/TitanCNA/extdata/test_tum_chr2.wig Slurping: /tmp/RtmpR2YV3E/Rinst3f48ec3c4ae151/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/RtmpR2YV3E/Rinst3f48ec3c4ae151/TitanCNA/extdata/test_norm_chr2.wig Slurping: /tmp/RtmpR2YV3E/Rinst3f48ec3c4ae151/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=-30461 and n=0.3971 (map), s=[0.0082,0.3756], phi=1.501 fwdBack: loglik=-34145.6617 fwdBack: priorN=0.3622 fwdBack: priorS=-2.6738 fwdBack: priorVar=-436.8800 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.0971 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 1 complete loglik=-34524.6068 fwdBack: Elapsed time for iteration 1: 0.0423m fwdBack: Iteration 2 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26832 and n=0.2539 (map), s=[0.0086,0.4329], phi=1.471 fwdBack: loglik=-28925.4753 fwdBack: priorN=0.1279 fwdBack: priorS=-2.5817 fwdBack: priorVar=-749.5778 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.2432 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 2 complete loglik=-29617.4064 fwdBack: Elapsed time for iteration 2: 0.0438m fwdBack: Iteration 3 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26076 and n=0.2114 (map), s=[0.0069,0.4528], phi=1.486 fwdBack: loglik=-26349.2019 fwdBack: priorN=0.0003 fwdBack: priorS=-2.7982 fwdBack: priorVar=-819.1445 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.1703 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 3 complete loglik=-27110.9710 fwdBack: Elapsed time for iteration 3: 0.0410m fwdBack: Total elapsed time: 0.2106m 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)