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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data FRASER
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* checking for file ‘FRASER/DESCRIPTION’ ... OK
* preparing ‘FRASER’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘FRASER.Rnw’ using knitr
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call2("C_viewSums_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
2: viewFun(as(x, "RleViews"), na.rm = na.rm)
3: viewFun(as(x, "RleViews"), na.rm = na.rm)
4: sum(new("CompressedRleList", elementType = "Rle", elementMetadata = NULL, metadata = list(), unlistData = new("Rle", values = logical(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), partitioning = new("PartitioningByEnd", end = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list())), na.rm = FALSE)
5: sum(new("CompressedRleList", elementType = "Rle", elementMetadata = NULL, metadata = list(), unlistData = new("Rle", values = logical(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), partitioning = new("PartitioningByEnd", end = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list())), na.rm = FALSE)
6: summarizeJunctions(galignment, genome = genome, with.revmap = (as.logical(strandMode) && pairedEnd))
7: FUN(...)
8: withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...)}, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition)}, warning = handle_warning)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning)}, error = identity)
13: FUN(X[[i]], ...)
14: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) || is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(X = c("chr3", "chr19", "chrUn_gl000218"), FUN = function (...) { if (!identical(timeout, WORKER_TIMEOUT)) { setTimeLimit(timeout, timeout, TRUE) on.exit(setTimeLimit(Inf, Inf, FALSE)) } if (!is.null(globalOptions)) base::options(globalOptions) if (stop.on.error && ERROR_OCCURRED) { UNEVALUATED } else { .rng_reset_generator("L'Ecuyer-CMRG", SEED) output <- tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning) }, error = identity) if (force.GC) gc(verbose = FALSE, full = FALSE) SEED <<- .rng_next_substream(SEED) output }}, bamFile = "/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample1.bam", pairedEnd = TRUE, genome = NULL, strandMode = 0, scanBamParam = new("ScanBamParam", flag = c(keep0 = 4095L, keep1 = 4095L), simpleCigar = FALSE, reverseComplement = FALSE, tag = character(0), tagFilter = list(), what = character(0), which = new("CompressedIRangesList", unlistData = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), elementType = "IRanges", elementMetadata = NULL, metadata = list(), partitioning = new("PartitioningByEnd", end = integer(0), NAMES = character(0), elementType = "ANY", elementMetadata = NULL, metadata = list())), mapqFilter = 0L))
15: do.call(lapply, args)
16: BiocParallel:::.workerLapply_impl(...)
17: (function (...) BiocParallel:::.workerLapply_impl(...))(X = c("chr3", "chr19", "chrUn_gl000218"), FUN = function (chromosome, bamFile, pairedEnd, strandMode, genome, scanBamParam) { which = GRanges(seqnames = chromosome, ranges = IRanges(0, 536870912)) param <- mergeBamParams(bamParam = scanBamParam, which = which) if (is.null(param)) { return(GRanges()) } if (isFALSE(as.logical(strandMode)) || isFALSE(pairedEnd)) { galignment <- readGAlignments(bamFile, param = param) } else { galignment <- readGAlignmentPairs(bamFile, param = param, strandMode = strandMode) } galignment <- galignment[!is.na(seqnames(galignment))] if (isFALSE(as.logical(strandMode))) { strand(galignment) <- "*" } if (isFALSE(pairedEnd) && strandMode == 2L) { galignment <- invertStrand(galignment) } if (length(galignment) == 0) { return(GRanges()) } if (!is.null(genome)) { if (is.character(genome)) { genome <- getBSgenome(genome) } if (any(seqlevelsStyle(galignment) != seqlevelsStyle(genome))) { warning("The seqlevelsStyles from the BAM file and the annotation", " are not the same! Will force annotation to use the one", " from the BAM file.") seqlevelsStyle(genome) <- seqlevelsStyle(galignment)[1] } chrLengths <- seqlengths(galignment) mismatchChrs <- which(seqlengths(genome)[names(chrLengths)] != chrLengths) if (length(mismatchChrs) > 0) { chrsToDrop <- names(chrLengths)[mismatchChrs] galignment <- dropSeqlevels(galignment, chrsToDrop) } } jc <- summarizeJunctions(galignment, genome = genome, with.revmap = (as.logical(strandMode) && pairedEnd)) if (length(jc) == 0) { return(GRanges()) } if (isTRUE(as.logical(strandMode))) { if (isTRUE(pairedEnd)) { fragment_counts <- vapply(jc@elementMetadata$revmap, FUN = function(pairs) { strands <- strand(galignment[pairs, ]) return(c(plus_score = sum(strands == "+"), minus_score = sum(strands == "-"))) }, FUN.VALUE = integer(2)) mcols(jc)[, "plus_score"] <- fragment_counts["plus_score", ] mcols(jc)[, "minus_score"] <- fragment_counts["minus_score", ] } jcPlus <- jc mcols(jcPlus)[, "score"] <- mcols(jc)[, "plus_score"] strand(jcPlus) <- "+" jcPlus <- jcPlus[mcols(jcPlus)[, "score"] > 0, ] jcMinus <- jc mcols(jcMinus)[, "score"] <- mcols(jc)[, "minus_score"] strand(jcMinus) <- "-" jcMinus <- jcMinus[mcols(jcMinus)[, "score"] > 0, ] jc <- c(jcPlus, jcMinus) } ans <- jc[, "score"] colnames(mcols(ans)) <- "count" if (isFALSE(as.logical(strandMode)) && !is.null(genome) && length(ans) > 0) { strand(ans) <- jc$intron_strand ans$intron_motif <- jc$intron_motif strand(ans)[jc$intron_strand == "*"] <- "+" } sort(ans)}, ARGS = list(bamFile = "/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample1.bam", pairedEnd = TRUE, genome = NULL, strandMode = 0, scanBamParam = new("ScanBamParam", flag = c(keep0 = 4095L, keep1 = 4095L), simpleCigar = FALSE, reverseComplement = FALSE, tag = character(0), tagFilter = list(), what = character(0), which = new("CompressedIRangesList", unlistData = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), elementType = "IRanges", elementMetadata = NULL, metadata = list(), partitioning = new("PartitioningByEnd", end = integer(0), NAMES = character(0), elementType = "ANY", elementMetadata = NULL, metadata = list())), mapqFilter = 0L)), OPTIONS = list(log = FALSE, threshold = "INFO", stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_, force.GC = FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, 1989395441L, -1801421250L, -1419308672L, -990181346L, 424009389L, 848918326L), GLOBALS = list(), PACKAGES = character(0))
18: do.call(msg$data$fun, msg$data$args)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ do.call(msg$data$fun, msg$data$args)}, error = function(e) { list(.error_worker_comm(e, "worker evaluation failed"))})
23: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
24: .recv_any(manager$backend)
25: .recv_any(manager$backend)
26: .manager_recv(manager)
27: .manager_recv(manager)
28: .collect_result(manager, reducer, progress, BPPARAM)
29: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length = length(redo_index))
30: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
31: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
32: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
33: bplapply(chromosomes, FUN = countSplitReadsPerChromosome, bamFile = bamfile, pairedEnd = pairedend, genome = genome, strandMode = strandmode, scanBamParam = scanbamparam, BPPARAM = getBPParam(NcpuPerSample, length(chromosomes)))
34: bplapply(chromosomes, FUN = countSplitReadsPerChromosome, bamFile = bamfile, pairedEnd = pairedend, genome = genome, strandMode = strandmode, scanBamParam = scanbamparam, BPPARAM = getBPParam(NcpuPerSample, length(chromosomes)))
35: FUN(...)
36: withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...)}, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition)}, warning = handle_warning)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning)}, error = identity)
41: FUN(X[[i]], ...)
42: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) || is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(X = c("sample1", "sample2", "sample3"), FUN = function (...) { if (!identical(timeout, WORKER_TIMEOUT)) { setTimeLimit(timeout, timeout, TRUE) on.exit(setTimeLimit(Inf, Inf, FALSE)) } if (!is.null(globalOptions)) base::options(globalOptions) if (stop.on.error && ERROR_OCCURRED) { UNEVALUATED } else { .rng_reset_generator("L'Ecuyer-CMRG", SEED) output <- tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning) }, error = identity) if (force.GC) gc(verbose = FALSE, full = FALSE) SEED <<- .rng_next_substream(SEED) output }}, fds = new("FraserDataSet", name = "Data Analysis", bamParam = new("ScanBamParam", flag = c(keep0 = 4095L, keep1 = 4095L), simpleCigar = FALSE, reverseComplement = FALSE, tag = character(0), tagFilter = list(), what = character(0), which = new("CompressedIRangesList", unlistData = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), elementType = "IRanges", elementMetadata = NULL, metadata = list(), partitioning = new("PartitioningByEnd", end = integer(0), NAMES = character(0), elementType = "ANY", elementMetadata = NULL, metadata = list())), mapqFilter = 0L), workingDir = "FRASER_output", nonSplicedReads = new("RangedSummarizedExperiment", rowRanges = new("GRanges", seqnames = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), strand = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), seqinfo = new("Seqinfo", seqnames = character(0), seqlengths = integer(0), is_circular = logical(0), genome = character(0)), elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), elementType = "ANY", metadata = list()), colData = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), assays = NULL, NAMES = NULL, elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), metadata = list()), rowRanges = new("GRanges", seqnames = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), strand = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), seqinfo = new("Seqinfo", seqnames = character(0), seqlengths = integer(0), is_circular = logical(0), genome = character(0)), elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), elementType = "ANY", metadata = list()), colData = new("DFrame", rownames = c("sample1", "sample2", "sample3"), nrows = 3L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list(sampleID = c("sample1", "sample2", "sample3"), bamFile = c("/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample1.bam", "/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample2.bam", "/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample3.bam" ), condition = c(1L, 3L, 2L), gene = c("TIMMDC1", "CLPP", "MCOLN1"), pairedEnd = c(TRUE, TRUE, TRUE))), assays = NULL, NAMES = NULL, elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), metadata = list( dontWriteHDF5 = TRUE)), NcpuPerSample = 1L, genome = NULL, recount = FALSE, keepNonStandardChromosomes = TRUE)
43: do.call(lapply, args)
44: BiocParallel:::.workerLapply_impl(...)
45: (function (...) BiocParallel:::.workerLapply_impl(...))(X = c("sample1", "sample2", "sample3"), FUN = function (sampleID, fds, NcpuPerSample = 1, genome = NULL, recount = FALSE, keepNonStandardChromosomes = TRUE, bamfile = bamFile(fds[, sampleID]), pairedend = pairedEnd(fds[, sampleID]), strandmode = strandSpecific(fds[, sampleID]), cacheFile = getSplitCountCacheFile(sampleID, fds), scanbamparam = scanBamParam(fds), coldata = colData(fds)) { validObject(fds) if (isFALSE(recount) && !is.null(cacheFile) && file.exists(cacheFile)) { cache <- readRDS(cacheFile) bamWhich <- unlist(bamWhich(scanbamparam)) if (length(bamWhich) > 0) { userTargetGR <- GRanges(seqnames = names(unlist(bamWhich)), ranges = unlist(bamWhich), strand = "*") from <- unique(from(findOverlaps(cache, userTargetGR))) cache <- cache[from] } if (length(cache) > 0) { message(date(), ": Using existing split read counts for sample: ", sampleID) if (isFALSE(keepNonStandardChromosomes)) { cache <- keepStandardChromosomes(cache, pruning.mode = "coarse") } return(checkSeqLevelStyle(gr = cache, sampleID = sampleID, sampleSpecific = FALSE, coldata = coldata)) } } message(date(), ": Count split reads for sample: ", sampleID) chromosomes <- extractChromosomes(bamfile) if (isFALSE(keepNonStandardChromosomes)) { chr_gr <- GRanges(seqnames = chromosomes, ranges = IRanges(1, 2)) chromosomes <- standardChromosomes(chr_gr) } if (is.character(genome) && length(genome) > 1) { genome <- genome[sampleID] } if (!is.null(genome)) { if (is.character(genome)) { genome <- getBSgenome(genome) } seqlevelsStyle(genome) <- seqlevelsStyle(chromosomes)[1] chrLengths <- extractChromosomeLengths(bamfile) mismatchChrs <- which(seqlengths(genome)[chromosomes] != chrLengths[chromosomes]) if (length(mismatchChrs) > 0) { warning("Not counting chromosome(s) ", paste(chromosomes[mismatchChrs], collapse = ", "), " in sample ", sampleID, " as it has a different length", " in the bamFile of this sample than in the provided", " genome.") chromosomes <- chromosomes[-mismatchChrs] } missingChrs <- which(!chromosomes %in% seqnames(genome)) if (length(missingChrs) > 0) { warning("Not counting chromosome(s) ", paste(chromosomes[missingChrs], collapse = ", "), " in sample ", sampleID, " as it is not specified in", " the provided genome.") chromosomes <- chromosomes[-missingChrs] } } countsList <- bplapply(chromosomes, FUN = countSplitReadsPerChromosome, bamFile = bamfile, pairedEnd = pairedend, genome = genome, strandMode = strandmode, scanBamParam = scanbamparam, BPPARAM = getBPParam(NcpuPerSample, length(chromosomes))) countsGR <- sort(unlist(GRangesList(countsList))) saveRDS(countsGR, cacheFile) return(checkSeqLevelStyle(gr = countsGR, sampleID = sampleID, sampleSpecific = FALSE, coldata = coldata))}, ARGS = list(fds = new("FraserDataSet", name = "Data Analysis", bamParam = new("ScanBamParam", flag = c(keep0 = 4095L, keep1 = 4095L ), simpleCigar = FALSE, reverseComplement = FALSE, tag = character(0), tagFilter = list(), what = character(0), which = new("CompressedIRangesList", unlistData = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), elementType = "IRanges", elementMetadata = NULL, metadata = list(), partitioning = new("PartitioningByEnd", end = integer(0), NAMES = character(0), elementType = "ANY", elementMetadata = NULL, metadata = list())), mapqFilter = 0L), workingDir = "FRASER_output", nonSplicedReads = new("RangedSummarizedExperiment", rowRanges = new("GRanges", seqnames = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), strand = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), seqinfo = new("Seqinfo", seqnames = character(0), seqlengths = integer(0), is_circular = logical(0), genome = character(0)), elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), elementType = "ANY", metadata = list()), colData = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), assays = NULL, NAMES = NULL, elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), metadata = list()), rowRanges = new("GRanges", seqnames = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = integer(0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), strand = new("Rle", values = integer(0), lengths = integer(0), elementMetadata = NULL, metadata = list()), seqinfo = new("Seqinfo", seqnames = character(0), seqlengths = integer(0), is_circular = logical(0), genome = character(0)), elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), elementType = "ANY", metadata = list()), colData = new("DFrame", rownames = c("sample1", "sample2", "sample3"), nrows = 3L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list(sampleID = c("sample1", "sample2", "sample3"), bamFile = c("/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample1.bam", "/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample2.bam", "/tmp/RtmprX1Tg4/Rinst3448965c1e25c5/FRASER/extdata/bam/sample3.bam" ), condition = c(1L, 3L, 2L), gene = c("TIMMDC1", "CLPP", "MCOLN1"), pairedEnd = c(TRUE, TRUE, TRUE))), assays = NULL, NAMES = NULL, elementMetadata = new("DFrame", rownames = NULL, nrows = 0L, elementType = "ANY", elementMetadata = NULL, metadata = list(), listData = list()), metadata = list( dontWriteHDF5 = TRUE)), NcpuPerSample = 1L, genome = NULL, recount = FALSE, keepNonStandardChromosomes = TRUE), OPTIONS = list( log = FALSE, threshold = "INFO", stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_, force.GC = FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, -1517153014L, 1989395441L, -1801421250L, 1955660617L, -990181346L, 424009389L), GLOBALS = list(), PACKAGES = character(0))
46: do.call(msg$data$fun, msg$data$args)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({ do.call(msg$data$fun, msg$data$args)}, error = function(e) { list(.error_worker_comm(e, "worker evaluation failed"))})
51: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
52: .recv_any(manager$backend)
53: .recv_any(manager$backend)
54: .manager_recv(manager)
55: .manager_recv(manager)
56: .collect_result(manager, reducer, progress, BPPARAM)
57: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length = length(redo_index))
58: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
59: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
60: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
61: bplapply(samples(fds), FUN = countSplitReads, fds = fds, BPPARAM = BPPARAM, NcpuPerSample = NcpuPerSample, genome = genome, recount = recount, keepNonStandardChromosomes = keepNonStandardChromosomes)
62: bplapply(samples(fds), FUN = countSplitReads, fds = fds, BPPARAM = BPPARAM, NcpuPerSample = NcpuPerSample, genome = genome, recount = recount, keepNonStandardChromosomes = keepNonStandardChromosomes)
63: getSplitReadCountsForAllSamples(fds = fds, NcpuPerSample = NcpuPerSample, junctionMap = junctionMap, recount = recount, BPPARAM = BPPARAM, genome = genome, keepNonStandardChromosomes = keepNonStandardChromosomes, outDir = file.path(countDir, "splitCounts"))
64: countRNAData(fds)
65: eval(expr, envir)
66: eval(expr, envir)
67: withVisible(eval(expr, envir))
68: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
69: eval(call)
70: eval(call)
71: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
72: doWithOneRestart(return(expr), restart)
73: withOneRestart(expr, restarts[[1L]])
74: withRestartList(expr, restarts[-nr])
75: doWithOneRestart(return(expr), restart)
76: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
77: withRestartList(expr, restarts)
78: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
79: evaluate::evaluate(...)
80: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
81: in_dir(input_dir(), expr)
82: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
83: eng_r(options)
84: block_exec(params)
85: call_block(x)
86: process_group(group)
87: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
88: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
89: process_file(text, output)
90: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
91: engine$weave(file, quiet = quiet, encoding = enc)
92: doTryCatch(return(expr), name, parentenv, handler)
93: tryCatchOne(expr, names, parentenv, handlers[[1L]])
94: tryCatchList(expr, classes, parentenv, handlers)
95: 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)))})
96: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
