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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount
###
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* checking for file ‘recount/DESCRIPTION’ ... OK
* preparing ‘recount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 1716 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpPhBQXQ/xshell62749a58887' 2>&1
ERROR
--- re-building ‘recount-quickstart.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
[WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata,
e.g. by using --metadata pagetitle="..." on the command line.
Falling back to 'SRP009615-results.knit'
*** caught segfault ***
address 0x701819d68, cause 'invalid permissions'
Traceback:
1: validObject(.Object)
2: disableValidity(old_val)
3: initialize(value, ...)
4: initialize(value, ...)
5: new(...)
6: new2("IRanges", start = start, width = width, check = FALSE)
7: .new_IRanges_from_end_width(end, width)
8: .new_IRanges(start = start, end = end, width = width)
9: IRanges(end = extractROWS(end(x@partitioning), i), width = ans_eltNROWS)
10: extractROWS(x, i)
11: extractROWS(x, i)
12: subset_along_ROWS(x, i, drop = drop)
13: which[names(which) %in% seqlevels(si)]
14: which[names(which) %in% seqlevels(si)]
15: .local(con, format, text, ...)
16: import(FileForFormat(con), ...)
17: import(FileForFormat(con), ...)
18: import(sampleFile, selection = reduce(regs), as = "RleList")
19: import(sampleFile, selection = reduce(regs), as = "RleList")
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(import(sampleFile, selection = reduce(regs), as = "RleList"), error = identity)
24: (function (sampleFile, mappedPerXM, L, chr, regs, verbose = TRUE) { if (verbose) message(paste(Sys.time(), "railMatrix: processing file", sampleFile)) N.TRIES <- 3L while (N.TRIES > 0L) { regCov <- tryCatch(import(sampleFile, selection = reduce(regs), as = "RleList"), error = identity) if (!inherits(regCov, "error")) { break } Sys.sleep(runif(n = 1, min = 2, max = 5)) N.TRIES <- N.TRIES - 1L } if (N.TRIES == 0L) stop(conditionMessage(regCov)) regCov <- regCov[[chr]] if (!is.null(mappedPerXM)) { regCov <- regCov/mappedPerXM } sum(Views(regCov, ranges(regs)))/L})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], chr = "chrY", regs = new("GRanges", seqnames = new("Rle", values = 1L, lengths = 808L, elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = c(2929794L, 2956678L, 2977203L, 2977957L, 2978850L, 2979004L, 2979077L, 2979181L, 2979829L, 2979913L, 2994977L, 2995103L, 2995240L, 2997474L, 2997680L, 3071363L, 3137046L, 3549320L, 3549382L, 3549509L, 3549653L, 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26595031L, 26614546L, 26614553L, 26614808L, 26626848L, 26627028L ), cluster = new("Rle", values = 1:225, lengths = c(1L, 1L, 8L, 5L, 1L, 1L, 7L, 1L, 1L, 12L, 8L, 1L, 1L, 15L, 1L, 1L, 2L, 1L, 1L, 10L, 13L, 11L, 1L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 22L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 20L, 2L, 2L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 7L, 1L, 1L, 20L, 107L, 50L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 1L, 5L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 7L, 2L, 1L, 12L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 11L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 17L, 2L, 4L, 18L, 1L, 1L, 18L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 12L, 1L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 4L, 5L, 8L, 15L, 3L, 1L, 10L, 3L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 9L, 3L, 13L, 17L, 4L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 8L, 1L, 1L, 35L, 3L, 2L), elementMetadata = NULL, metadata = list()), clusterL = new("Rle", values = c(36, 24, 2750, 2705, 16, 50, 722, 22, 37, 3179, 2031, 29, 1, 3730, 20, 72, 6, 27, 30, 1451, 1330, 1289, 36, 476, 10, 40, 39, 27, 66, 31, 172, 23, 59, 762, 25, 46, 149, 8, 98, 33, 9512, 33, 21, 35, 730, 37, 1991, 33, 36, 66, 38, 24, 30, 31, 41, 29, 8, 25, 1621, 4817, 11, 2375, 5565, 37, 19, 24, 22, 26, 28, 31, 15, 26, 34, 5, 85, 18, 5632, 37, 84, 3386, 30017, 18562, 4274, 32, 33, 36, 46, 31, 52, 14, 36, 33, 4371, 35, 27, 4129, 16, 29, 35, 307, 36, 33, 43, 38, 29, 128, 4813, 2282, 29, 6309, 1058, 59, 36, 39, 7, 48, 26, 93, 523, 187, 45, 2315, 29, 26, 34, 29, 45, 1070, 36, 33, 744, 29, 14, 24, 48, 50, 13, 40, 36, 22, 32, 36, 37, 29, 2, 23, 27, 385, 34, 3989, 718, 963, 4174, 32, 21, 2152, 38, 1529, 175, 36, 38, 5, 35, 37, 8145, 26, 951, 36, 10, 35, 20, 38, 35, 25, 29, 14, 18, 38, 114, 879, 1016, 1788, 1754, 1456, 5500, 2306, 19, 4255, 19, 388, 26, 33, 17, 29, 7, 29, 32, 382, 26, 1377, 1875, 5497, 6344, 1788, 14, 1422, 44, 18, 38, 36, 27, 5, 11, 20, 36, 39, 1097, 2718, 36, 34, 8719, 298, 221), lengths = c(1L, 1L, 8L, 5L, 1L, 1L, 7L, 1L, 1L, 12L, 8L, 1L, 1L, 15L, 1L, 1L, 2L, 1L, 1L, 10L, 13L, 11L, 1L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 22L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 20L, 2L, 2L, 4L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 7L, 1L, 1L, 20L, 107L, 50L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 1L, 5L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 7L, 2L, 1L, 12L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 11L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 17L, 2L, 4L, 18L, 1L, 1L, 18L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 12L, 1L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 4L, 5L, 8L, 15L, 3L, 1L, 10L, 3L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 9L, 3L, 13L, 17L, 4L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 8L, 1L, 1L, 35L, 3L, 2L), elementMetadata = NULL, metadata = list()))), elementType = "ANY", metadata = list()), verbose = TRUE)
25: .mapply(.FUN, dots, .MoreArgs)
26: FUN(...)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch({ FUN(...)}, error = handle_error)
31: withCallingHandlers({ tryCatch({ FUN(...) }, error = handle_error)}, warning = handle_warning)
32: FUN(X[[i]], ...)
33: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) || is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(X = 1:12, 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 <- withCallingHandlers({ tryCatch({ FUN(...) }, error = handle_error) }, warning = handle_warning) if (force.GC) gc(verbose = FALSE, full = FALSE) SEED <<- .rng_next_substream(SEED) output }}, .FUN = function (sampleFile, mappedPerXM, L, chr, regs, verbose = TRUE) { if (verbose) message(paste(Sys.time(), "railMatrix: processing file", sampleFile)) N.TRIES <- 3L while (N.TRIES > 0L) { regCov <- tryCatch(import(sampleFile, selection = reduce(regs), as = "RleList"), error = identity) if (!inherits(regCov, "error")) { break } Sys.sleep(runif(n = 1, min = 2, max = 5)) N.TRIES <- N.TRIES - 1L } if (N.TRIES == 0L) stop(conditionMessage(regCov)) regCov <- regCov[[chr]] if (!is.null(mappedPerXM)) { regCov <- regCov/mappedPerXM } sum(Views(regCov, ranges(regs)))/L}, .ddd = list(c("http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw"), c(25.737361125, 29.621949625, 33.413224225, 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26404436L, 26515694L, 26526628L, 26527635L, 26527696L, 26534469L, 26535380L, 26535395L, 26536218L, 26536486L, 26536906L, 26536930L, 26537149L, 26549895L, 26579755L, 26586335L, 26586756L, 26587429L, 26589592L, 26589652L, 26589986L, 26590301L, 26590470L, 26590582L, 26590712L, 26590890L, 26591198L, 26591413L, 26591610L, 26591733L, 26591806L, 26591861L, 26591935L, 26592269L, 26592507L, 26592675L, 26592780L, 26592894L, 26592940L, 26593064L, 26593261L, 26593323L, 26593398L, 26593778L, 26594043L, 26594164L, 26594321L, 26594443L, 26594606L, 26595031L, 26614546L, 26614553L, 26614808L, 26626848L, 26627028L), cluster = new("Rle", values = 1:225, lengths = c(1L, 1L, 8L, 5L, 1L, 1L, 7L, 1L, 1L, 12L, 8L, 1L, 1L, 15L, 1L, 1L, 2L, 1L, 1L, 10L, 13L, 11L, 1L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 22L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 20L, 2L, 2L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 7L, 1L, 1L, 20L, 107L, 50L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 1L, 5L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 7L, 2L, 1L, 12L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 11L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 17L, 2L, 4L, 18L, 1L, 1L, 18L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 12L, 1L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 4L, 5L, 8L, 15L, 3L, 1L, 10L, 3L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 9L, 3L, 13L, 17L, 4L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 8L, 1L, 1L, 35L, 3L, 2L), elementMetadata = NULL, metadata = list()), clusterL = new("Rle", values = c(36, 24, 2750, 2705, 16, 50, 722, 22, 37, 3179, 2031, 29, 1, 3730, 20, 72, 6, 27, 30, 1451, 1330, 1289, 36, 476, 10, 40, 39, 27, 66, 31, 172, 23, 59, 762, 25, 46, 149, 8, 98, 33, 9512, 33, 21, 35, 730, 37, 1991, 33, 36, 66, 38, 24, 30, 31, 41, 29, 8, 25, 1621, 4817, 11, 2375, 5565, 37, 19, 24, 22, 26, 28, 31, 15, 26, 34, 5, 85, 18, 5632, 37, 84, 3386, 30017, 18562, 4274, 32, 33, 36, 46, 31, 52, 14, 36, 33, 4371, 35, 27, 4129, 16, 29, 35, 307, 36, 33, 43, 38, 29, 128, 4813, 2282, 29, 6309, 1058, 59, 36, 39, 7, 48, 26, 93, 523, 187, 45, 2315, 29, 26, 34, 29, 45, 1070, 36, 33, 744, 29, 14, 24, 48, 50, 13, 40, 36, 22, 32, 36, 37, 29, 2, 23, 27, 385, 34, 3989, 718, 963, 4174, 32, 21, 2152, 38, 1529, 175, 36, 38, 5, 35, 37, 8145, 26, 951, 36, 10, 35, 20, 38, 35, 25, 29, 14, 18, 38, 114, 879, 1016, 1788, 1754, 1456, 5500, 2306, 19, 4255, 19, 388, 26, 33, 17, 29, 7, 29, 32, 382, 26, 1377, 1875, 5497, 6344, 1788, 14, 1422, 44, 18, 38, 36, 27, 5, 11, 20, 36, 39, 1097, 2718, 36, 34, 8719, 298, 221), lengths = c(1L, 1L, 8L, 5L, 1L, 1L, 7L, 1L, 1L, 12L, 8L, 1L, 1L, 15L, 1L, 1L, 2L, 1L, 1L, 10L, 13L, 11L, 1L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 22L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 20L, 2L, 2L, 4L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 7L, 1L, 1L, 20L, 107L, 50L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 1L, 5L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 7L, 2L, 1L, 12L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 11L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 17L, 2L, 4L, 18L, 1L, 1L, 18L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 12L, 1L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 4L, 5L, 8L, 15L, 3L, 1L, 10L, 3L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 9L, 3L, 13L, 17L, 4L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 8L, 1L, 1L, 35L, 3L, 2L), elementMetadata = NULL, metadata = list()))), elementType = "ANY", metadata = list()), verbose = TRUE))
34: do.call(lapply, args)
35: BiocParallel:::.workerLapply_impl(...)
36: (function (...) BiocParallel:::.workerLapply_impl(...))(X = 1:12, FUN = function (.i, .FUN, .ddd, .MoreArgs) { dots <- lapply(.ddd, `[`, .i) .mapply(.FUN, dots, .MoreArgs)[[1L]]}, ARGS = list(.FUN = function (sampleFile, mappedPerXM, L, chr, regs, verbose = TRUE) { if (verbose) message(paste(Sys.time(), "railMatrix: processing file", sampleFile)) N.TRIES <- 3L while (N.TRIES > 0L) { regCov <- tryCatch(import(sampleFile, selection = reduce(regs), as = "RleList"), error = identity) if (!inherits(regCov, "error")) { break } Sys.sleep(runif(n = 1, min = 2, max = 5)) N.TRIES <- N.TRIES - 1L } if (N.TRIES == 0L) stop(conditionMessage(regCov)) regCov <- regCov[[chr]] if (!is.null(mappedPerXM)) { regCov <- regCov/mappedPerXM } sum(Views(regCov, ranges(regs)))/L}, .ddd = list(c("http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw", "http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw"), c(25.737361125, 29.621949625, 33.413224225, 26.8294529, 22.349458875, 25.23042305, 42.9844605, 29.088198475, 19.542148875, 15.401221325, 20.15808365, 19.69489275), c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .MoreArgs = list(chr = "chrY", regs = new("GRanges", seqnames = new("Rle", values = 1L, lengths = 808L, elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = c(2929794L, 2956678L, 2977203L, 2977957L, 2978850L, 2979004L, 2979077L, 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2L, 4L, 5L, 8L, 15L, 3L, 1L, 10L, 3L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 9L, 3L, 13L, 17L, 4L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 8L, 1L, 1L, 35L, 3L, 2L), elementMetadata = NULL, metadata = list()))), elementType = "ANY", metadata = list()), verbose = 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, 735270329L, 693045798L, 569708143L, -1318637084L, 2131724181L, 283583314L ), GLOBALS = list(), PACKAGES = character(0))
37: do.call(msg$data$fun, msg$data$args)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch({ do.call(msg$data$fun, msg$data$args)}, error = function(e) { list(.error_worker_comm(e, "worker evaluation failed"))})
42: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
43: .recv_any(manager$backend)
44: .recv_any(manager$backend)
45: .manager_recv(manager)
46: .manager_recv(manager)
47: .collect_result(manager, reducer, progress, BPPARAM)
48: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length = length(redo_index))
49: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
50: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
51: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
52: bplapply(X = seq_along(ddd[[1L]]), .wrap, .FUN = FUN, .ddd = ddd, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
53: bplapply(X = seq_along(ddd[[1L]]), .wrap, .FUN = FUN, .ddd = ddd, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
54: bpmapply(.railMatChrRegionCov, sampleFiles, mappedPerXM, L, BPPARAM = BPPARAM.railChr, MoreArgs = list(chr = chr, regs = regions, verbose = verboseLoad))
55: bpmapply(.railMatChrRegionCov, sampleFiles, mappedPerXM, L, BPPARAM = BPPARAM.railChr, MoreArgs = list(chr = chr, regs = regions, verbose = verboseLoad))
56: FUN(X[[i]], ...)
57: lapply(regs_split, derfinder:::.railMatChrRegion, sampleFiles = sampleFiles, chr = chr, mappedPerXM = mappedPerXM, L = 1, verbose = verbose, BPPARAM.railChr = bpparam, verboseLoad = verboseLoad, chrlen = chrlen)
58: lapply(regs_split, derfinder:::.railMatChrRegion, sampleFiles = sampleFiles, chr = chr, mappedPerXM = mappedPerXM, L = 1, verbose = verbose, BPPARAM.railChr = bpparam, verboseLoad = verboseLoad, chrlen = chrlen)
59: coverage_matrix("SRP009615", "chrY", regions)
60: system.time(rse_ER <- coverage_matrix("SRP009615", "chrY", regions))
61: eval(expr, envir, enclos)
62: eval(expr, envir, enclos)
63: eval_with_user_handlers(expr, envir, enclos, user_handlers)
64: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
65: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
66: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
67: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
68: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
69: evaluate::evaluate(...)
70: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$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$render, options))
71: in_dir(input_dir(), expr)
72: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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)))
73: eng_r(options)
74: block_exec(params)
75: call_block(x)
76: process_group.block(group)
77: process_group(group)
78: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
79: process_file(text, output)
80: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
81: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
82: vweave_rmarkdown(...)
83: engine$weave(file, quiet = quiet, encoding = enc)
84: doTryCatch(return(expr), name, parentenv, handler)
85: tryCatchOne(expr, names, parentenv, handlers[[1L]])
86: tryCatchList(expr, classes, parentenv, handlers)
87: 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)))})
88: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...