############################################################################## ############################################################################## ### ### 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/RtmpKkNMHQ/Rinst2c40183adca59b/TitanCNA/extdata/test_alleleCounts_chr2.txt Reading GC and mappability files Slurping: /tmp/RtmpKkNMHQ/Rinst2c40183adca59b/TitanCNA/extdata/gc_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Slurping: /tmp/RtmpKkNMHQ/Rinst2c40183adca59b/TitanCNA/extdata/map_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Loading tumour file:/tmp/RtmpKkNMHQ/Rinst2c40183adca59b/TitanCNA/extdata/test_tum_chr2.wig Slurping: /tmp/RtmpKkNMHQ/Rinst2c40183adca59b/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/RtmpKkNMHQ/Rinst2c40183adca59b/TitanCNA/extdata/test_norm_chr2.wig Slurping: /tmp/RtmpKkNMHQ/Rinst2c40183adca59b/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=-30486 and n=0.3983 (map), s=[0.0083,0.3767], phi=1.503 fwdBack: loglik=-34146.9581 fwdBack: priorN=0.3632 fwdBack: priorS=-2.6666 fwdBack: priorVar=-437.7122 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.0892 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 1 complete loglik=-34526.7193 fwdBack: Elapsed time for iteration 1: 0.0421m fwdBack: Iteration 2 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26835 and n=0.2537 (map), s=[0.0091,0.4330], phi=1.469 fwdBack: loglik=-28978.1873 fwdBack: priorN=0.1276 fwdBack: priorS=-2.5328 fwdBack: priorVar=-749.0091 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.2527 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 2 complete loglik=-29669.5108 fwdBack: Elapsed time for iteration 2: 0.0408m fwdBack: Iteration 3 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26080 and n=0.2115 (map), s=[0.0069,0.4527], phi=1.484 fwdBack: loglik=-26352.8255 fwdBack: priorN=0.0007 fwdBack: priorS=-2.7964 fwdBack: priorVar=-818.1292 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.1795 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 3 complete loglik=-27113.5863 fwdBack: Elapsed time for iteration 3: 0.0404m fwdBack: Total elapsed time: 0.2062m 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)