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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, 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25460137L, 25460528L, 25460666L, 25461996L, 25462078L,                 25462194L, 25462252L, 25462296L, 25462304L, 25462367L,                 25462465L, 25462660L, 25465564L, 25488356L, 25488695L,                 25488763L, 25488795L, 25488868L, 25488890L, 25488991L,                 25489018L, 25489031L, 25489049L, 25489080L, 25489094L,                 25490897L, 25493483L, 25493539L, 25494303L, 25494660L,                 25497847L, 25497898L, 25499200L, 25499592L, 25508820L,                 25512302L, 25513687L, 25527658L, 25783770L, 25861487L,                 25918431L, 26208087L, 26328981L, 26337463L, 26348502L,                 26404401L, 26515656L, 26526600L, 26527618L, 26527674L,                 26534432L, 26535380L, 26535387L, 26536179L, 26536473L,                 26536906L, 26536913L, 26537117L, 26549860L, 26579722L,                 26586313L, 26586722L, 26587405L, 26589544L, 26589603L,                 26589920L, 26590261L, 26590421L, 26590509L, 26590669L,                 26590821L, 26591156L, 26591380L, 26591534L, 26591693L,                 26591753L, 26591815L, 26591900L, 26592218L, 26592472L,                 26592616L, 26592745L, 26592826L, 26592908L, 26593012L,                 26593178L, 26593283L, 26593354L, 26593741L, 26593984L,                 26594111L, 26594293L, 26594396L, 26594557L, 26594996L,                 26614511L, 26614548L, 26614779L, 26626808L, 26626971L                ), indexEnd = c(2929829L, 2956701L, 2977227L,                 2977994L, 2978871L, 2979033L, 2979110L, 2979231L,                 2979870L, 2979952L, 2995015L, 2995144L, 2995273L,                 2997511L, 2997681L, 3071378L, 3137095L, 3549339L,                 3549410L, 3549545L, 3549668L, 3549722L, 3549912L,                 3550041L, 3583423L, 3622433L, 3682797L, 3682917L,                 3683061L, 3683425L, 3683476L, 3683579L, 3683704L,                 3683968L, 3684087L, 3684337L, 3684462L, 3685965L,                 3864675L, 3864853L, 3865449L, 3865577L, 3865675L,                 3866002L, 3866066L, 3866670L, 3966387L, 4036399L,                 4042451L, 4044271L, 4044278L, 4044327L, 4044340L,                 4044496L, 4044498L, 4044500L, 4044530L, 4044617L,                 4045051L, 4045056L, 4045072L, 4046173L, 4046176L,                 4217730L, 4344851L, 4356018L, 4356021L, 4360809L,                 4801125L, 5206558L, 5206675L, 5206829L, 5206901L,                 5207301L, 5207365L, 5207529L, 5207625L, 5207835L,                 5207955L, 5337651L, 5337766L, 5337883L, 5337980L,                 5338139L, 5338200L, 5338293L, 5338409L, 5338546L,                 5338715L, 5338826L, 5338895L, 5338941L, 5573256L,                 5573508L, 5573583L, 5573647L, 5573718L, 5573823L,                 5573870L, 5573908L, 5574100L, 5574374L, 5574478L,                 5634625L, 5793319L, 5793478L, 5793658L, 5793750L,                 5815563L, 5888018L, 6124459L, 6142036L, 6719031L,                 6893764L, 6901235L, 6901349L, 6949120L, 7070782L,                 7080089L, 7080817L, 7107149L, 7133958L, 7304025L,                 7304093L, 7326169L, 7341212L, 7356184L, 7371855L,                 7372755L, 7372826L, 7373060L, 7373213L, 7374622L,                 7375777L, 7378389L, 7378498L, 7378509L, 7378516L,                 7378634L, 7378731L, 7378919L, 7379968L, 7380059L,                 7380194L, 7380547L, 7380642L, 7380746L, 7381087L,                 7381345L, 7501949L, 7621337L, 7621353L, 7666382L,                 8538316L, 8539010L, 8543615L, 8648171L, 8650111L,                 8717704L, 8871329L, 9141961L, 9187807L, 9560331L,                 9560354L, 9671927L, 9988268L, 10088100L, 10091525L,                 10094663L, 10173682L, 10190490L, 10190643L, 10190846L,                 10191525L, 10191805L, 10192086L, 10195470L, 10195948L,                 10196275L, 10197377L, 10197520L, 10197823L, 10197879L,                 10197890L, 10198161L, 10198328L, 10198487L, 10198489L,                 10198571L, 10198667L, 10198799L, 10198885L, 10198889L,                 10198979L, 10199065L, 10200282L, 10667003L, 10667011L,                 10774060L, 10776411L, 10796143L, 10796350L, 10799307L,                 10801662L, 10808038L, 10863083L, 10874678L, 10967562L,                 10973618L, 10976935L, 10983080L, 10991247L, 10999930L,                 11006922L, 11023305L, 11031609L, 11110816L, 11113991L,                 11113995L, 11121716L, 11121870L, 11121881L, 11121890L,                 11123707L, 11124305L, 11127346L, 11134838L, 11144384L,                 11153881L, 11153982L, 11154110L, 11154185L, 11154413L,                 11154516L, 11154694L, 11154740L, 11154817L, 11154965L,                 11155227L, 11155289L, 11155302L, 11155328L, 11155408L,                 11155414L, 11155451L, 11155779L, 11155884L, 11157201L,                 11161917L, 11161927L, 11161930L, 11162036L, 11162102L,                 11162229L, 11162409L, 11162492L, 11162630L, 11162861L,                 11163057L, 11163139L, 11163218L, 11163873L, 11164024L,                 11164704L, 11164734L, 11164768L, 11165210L, 11165217L,                 11165445L, 11165800L, 11166029L, 11166087L, 11166361L,                 11166418L, 11166472L, 11166657L, 11166686L, 11166689L,                 11166718L, 11166732L, 11166779L, 11166887L, 11166999L,                 11167128L, 11167234L, 11167268L, 11167291L, 11167356L,                 11167526L, 11167590L, 11167609L, 11167702L, 11167892L,                 11168091L, 11168095L, 11168278L, 11168289L, 11168299L,                 11168301L, 11168307L, 11168462L, 11168629L, 11169498L,                 11169550L, 11169901L, 11170045L, 11170157L, 11170312L,                 11171074L, 11173458L, 11173614L, 11173727L, 11173732L,                 11173747L, 11174488L, 11175804L, 11176263L, 11176265L,                 11176389L, 11176391L, 11176408L, 11176410L, 11177652L,                 11178128L, 11179575L, 11179603L, 11179684L, 11179688L,                 11180032L, 11180423L, 11182918L, 11183388L, 11184235L,                 11184436L, 11184893L, 11185263L, 11185278L, 11185903L,                 11186140L, 11186454L, 11186463L, 11186471L, 11186602L,                 11188462L, 11189537L, 11189544L, 11189552L, 11189561L,                 11189641L, 11189801L, 11190500L, 11191256L, 11191265L,                 11191922L, 11191932L, 11196440L, 11196444L, 11197336L,                 11197615L, 11199159L, 11200312L, 11200412L, 11200735L,                 11201489L, 11201700L, 11202740L, 11203066L, 11203381L,                 11203392L, 11203400L, 11203435L, 11203442L, 11203535L,                 11203539L, 11203599L, 11203613L, 11203632L, 11203745L,                 11203922L, 11204126L, 11204191L, 11204233L, 11204242L,                 11204483L, 11204492L, 11205055L, 11205124L, 11205279L,                 11205312L, 11205316L, 11205524L, 11205737L, 11205753L,                 11206247L, 11206258L, 11206323L, 11206452L, 11206641L,                 11208224L, 11209289L, 11209720L, 11212482L, 11212802L,                 11214307L, 11214975L, 11298868L, 11301496L, 11302755L,                 11302757L, 11302793L, 11303125L, 11338072L, 11417445L,                 11502609L, 11722039L, 11734890L, 11747728L, 11790858L,                 11886830L, 11923572L, 12148280L, 12149661L, 12149967L,                 12150288L, 12152619L, 12163962L, 12245324L, 12318978L,                 12319678L, 12322618L, 12322833L, 12323065L, 12375489L,                 12375501L, 12473458L, 12567503L, 12577677L, 12577945L,                 12757295L, 12773703L, 12790464L, 12810240L, 12818561L,                 12842369L, 12856716L, 12856837L, 12915214L, 12915774L,                 12918114L, 12918185L, 12919530L, 12919878L, 12919971L,                 13118297L, 13120534L, 13160108L, 13282872L, 13283018L,                 13285658L, 13286767L, 13286838L, 13286959L, 13287016L,                 13287088L, 13287350L, 13287440L, 13287533L, 13289146L,                 13323678L, 13323722L, 13324695L, 13350684L, 13359132L,                 13464941L, 13635010L, 13704400L, 13718430L, 13819702L,                 13819758L, 13986094L, 13986433L, 14056819L, 14133902L,                 14313556L, 14314109L, 14315834L, 14511792L, 14588841L,                 14597626L, 14639547L, 14907999L, 14940754L, 14940875L,                 14940929L, 14941002L, 14941122L, 14941171L, 14941315L,                 14941384L, 14941475L, 14941684L, 14941786L, 15259478L,                 15291869L, 15434392L, 15435128L, 15513996L, 15537780L,                 15835054L, 15883024L, 15896816L, 16100366L, 16203160L,                 16382216L, 16493395L, 16504262L, 16694452L, 16831914L,                 16835231L, 16977370L, 17186921L, 17349252L, 17580083L,                 17580447L, 17592375L, 17610149L, 17610595L, 17610895L,                 17611034L, 17611157L, 17611297L, 17611386L, 17611779L,                 17611813L, 17611821L, 17611951L, 17612056L, 17612559L,                 17612667L, 17612955L, 17614060L, 17614099L, 17756731L,                 17757405L, 18148384L, 18148639L, 18148750L, 18149321L,                 18291752L, 18291972L, 18291978L, 18292830L, 18293109L,                 18293375L, 18293994L, 18294135L, 18294214L, 18294221L,                 18294290L, 18294670L, 18294781L, 18294893L, 18295024L,                 18295147L, 18295463L, 18295898L, 18313663L, 18325944L,                 18990708L, 18990759L, 18990974L, 18991077L, 18991193L,                 18991275L, 18991378L, 18991569L, 18991650L, 18991717L,                 18991776L, 18991847L, 18991954L, 18992110L, 18992432L,                 18992569L, 18992675L, 18992798L, 19276928L, 19419576L,                 19421069L, 19707586L, 19707727L, 19919514L, 19986361L,                 20006458L, 20355826L, 20582626L, 20643400L, 20646092L,                 20647866L, 20648223L, 20648651L, 20649173L, 20649867L,                 20649971L, 20650229L, 20651193L, 20651298L, 20651506L,                 20902171L, 20906251L, 20906895L, 20907171L, 21042123L,                 21408415L, 21408418L, 21572334L, 21646242L, 21675877L,                 21857493L, 22774410L, 22943045L, 23341323L, 23462518L,                 23808602L, 24142374L, 24142477L, 24155578L, 24156454L,                 24160319L, 24161327L, 24170554L, 24170943L, 24172235L,                 24172298L, 24175476L, 24175835L, 24176609L, 24176662L,                 24177204L, 24180355L, 24181110L, 24181149L, 24181277L,                 24181365L, 24181388L, 24181458L, 24181782L, 24204541L,                 24207486L, 24207771L, 24207836L, 24207846L, 24207851L,                 24207890L, 24207951L, 24207958L, 24208079L, 24208082L,                 24208105L, 24208126L, 24209471L, 24210006L, 24213293L,                 24214992L, 24215549L, 24270151L, 24275981L, 24275987L,                 24276009L, 24276282L, 24276936L, 24277222L, 24277277L,                 24277292L, 24277309L, 24280206L, 24305546L, 24305555L,                 24305561L, 24362141L, 24362281L, 24362361L, 24362432L,                 24408153L, 24428463L, 24576795L, 24951649L, 24956975L,                 25093322L, 25241682L, 25307756L, 25307854L, 25307892L,                 25307971L, 25308093L, 25364602L, 25392857L, 25392909L,                 25392970L, 25393268L, 25393614L, 25393637L, 25393899L,                 25394150L, 25394199L, 25455050L, 25455192L, 25456889L,                 25460175L, 25460548L, 25460718L, 25461996L, 25462117L,                 25462226L, 25462292L, 25462297L, 25462335L, 25462387L,                 25462483L, 25462694L, 25465633L, 25488391L, 25488718L,                 25488770L, 25488825L, 25488887L, 25488897L, 25489014L,                 25489018L, 25489033L, 25489051L, 25489084L, 25489099L,                 25490915L, 25493518L, 25493607L, 25494339L, 25494699L,                 25497872L, 25497933L, 25499242L, 25499634L, 25508833L,                 25512336L, 25513723L, 25527701L, 25783787L, 25861524L,                 25918466L, 26208113L, 26328985L, 26337473L, 26348521L,                 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)
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, 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,     2979181L, 2979829L, 2979913L, 2994977L, 2995103L, 2995240L,     2997474L, 2997680L, 3071363L, 3137046L, 3549320L, 3549382L,     3549509L, 3549653L, 3549683L, 3549875L, 3549969L, 3583402L,     3622397L, 3682787L, 3682881L, 3683028L, 3683339L, 3683455L,     3683553L, 3683631L, 3683938L, 3684051L, 3684288L, 3684454L,     3685945L, 3864640L, 3864772L, 3865407L, 3865531L, 3865639L,     3865954L, 3866022L, 3866613L, 3966359L, 4036399L, 4042447L,     4044209L, 4044273L, 4044323L, 4044329L, 4044495L, 4044498L,     4044500L, 4044502L, 4044606L, 4045045L, 4045056L, 4045067L,     4046148L, 4046175L, 4217711L, 4344780L, 4356016L, 4356021L,     4360783L, 4801096L, 5206505L, 5206637L, 5206791L, 5206856L,     5207125L, 5207319L, 5207492L, 5207588L, 5207761L, 5207848L,     5337612L, 5337731L, 5337813L, 5337885L, 5338099L, 5338142L,     5338223L, 5338324L, 5338488L, 5338595L, 5338784L, 5338829L,     5338905L, 5573190L, 5573459L, 5573537L, 5573601L, 5573662L,     5573783L, 5573833L, 5573873L, 5574020L, 5574312L, 5574409L,     5634590L, 5793275L, 5793393L, 5793630L, 5793711L, 5815554L,     5887979L, 6124421L, 6142010L, 6718966L, 6893734L, 6901178L,     6901326L, 6949098L, 7070724L, 7080056L, 7080787L, 7107125L,     7133913L, 7303945L, 7304066L, 7326162L, 7341115L, 7356152L,     7371834L, 7372736L, 7372792L, 7373039L, 7373152L, 7374598L,     7375717L, 7378345L, 7378442L, 7378500L, 7378513L, 7378519L,     7378682L, 7378918L, 7379917L, 7380054L, 7380156L, 7380520L,     7380607L, 7380684L, 7381057L, 7381323L, 7501917L, 7621333L,     7621353L, 7666348L, 8538281L, 8538962L, 8543579L, 8648121L,     8650076L, 8717672L, 8871294L, 9141896L, 9187770L, 9560331L,     9560336L, 9671898L, 9988238L, 10088060L, 10091497L, 10094656L,     10173658L, 10190466L, 10190619L, 10190827L, 10191518L, 10191724L,     10192023L, 10195466L, 10195913L, 10196255L, 10197279L, 10197465L,     10197773L, 10197839L, 10197881L, 10198128L, 10198220L, 10198404L,     10198489L, 10198498L, 10198581L, 10198705L, 10198837L, 10198887L,     10198954L, 10199025L, 10200164L, 10667001L, 10667011L, 10774037L,     10776378L, 10796098L, 10796321L, 10799279L, 10801634L, 10808002L,     10863065L, 10874655L, 10967541L, 10973593L, 10976908L, 10983053L,     10991217L, 10999916L, 11006897L, 11023272L, 11031605L, 11110732L,     11113978L, 11113994L, 11121715L, 11121866L, 11121874L, 11121888L,     11123706L, 11124283L, 11127303L, 11134802L, 11144301L, 11153816L,     11153951L, 11154065L, 11154142L, 11154369L, 11154486L, 11154654L,     11154696L, 11154787L, 11154922L, 11155227L, 11155229L, 11155291L,     11155317L, 11155404L, 11155411L, 11155416L, 11155735L, 11155832L,     11157189L, 11161916L, 11161926L, 11161930L, 11161942L, 11162068L,     11162116L, 11162272L, 11162457L, 11162531L, 11162675L, 11162907L,     11163076L, 11163188L, 11163862L, 11163995L, 11164683L, 11164733L,     11164736L, 11165202L, 11165216L, 11165407L, 11165760L, 11166003L,     11166066L, 11166210L, 11166411L, 11166470L, 11166606L, 11166686L,     11166688L, 11166694L, 11166721L, 11166738L, 11166852L, 11166964L,     11167032L, 11167161L, 11167268L, 11167275L, 11167321L, 11167371L,     11167586L, 11167596L, 11167681L, 11167837L, 11168070L, 11168095L,     11168227L, 11168289L, 11168297L, 11168301L, 11168303L, 11168365L,     11168612L, 11169463L, 11169516L, 11169883L, 11170043L, 11170047L,     11170303L, 11171051L, 11173437L, 11173571L, 11173718L, 11173729L,     11173744L, 11174462L, 11175775L, 11176262L, 11176265L, 11176380L,     11176391L, 11176395L, 11176410L, 11177651L, 11178128L, 11179568L,     11179579L, 11179678L, 11179688L, 11180029L, 11180418L, 11182918L,     11183386L, 11184223L, 11184436L, 11184887L, 11185254L, 11185265L,     11185881L, 11186112L, 11186454L, 11186460L, 11186467L, 11186592L,     11188462L, 11189533L, 11189543L, 11189551L, 11189554L, 11189612L,     11189752L, 11190475L, 11191254L, 11191263L, 11191918L, 11191930L,     11196414L, 11196443L, 11197333L, 11197592L, 11199130L, 11200287L,     11200412L, 11200686L, 11201454L, 11201700L, 11202699L, 11203054L,     11203327L, 11203386L, 11203400L, 11203411L, 11203442L, 11203465L,     11203537L, 11203597L, 11203612L, 11203630L, 11203723L, 11203868L,     11204091L, 11204156L, 11204230L, 11204242L, 11204468L, 11204487L,     11205016L, 11205081L, 11205279L, 11205281L, 11205315L, 11205520L,     11205700L, 11205753L, 11206145L, 11206250L, 11206262L, 11206448L,     11206599L, 11208206L, 11209273L, 11209685L, 11212455L, 11212744L,     11214272L, 11214938L, 11298852L, 11301482L, 11302752L, 11302757L,     11302759L, 11303090L, 11338041L, 11417413L, 11502574L, 11721994L,     11734860L, 11747677L, 11790845L, 11886795L, 11923540L, 12148249L,     12149622L, 12149936L, 12150258L, 12152615L, 12163928L, 12245298L,     12318937L, 12319643L, 12322580L, 12322791L, 12323039L, 12375486L,     12375491L, 12473430L, 12567469L, 12577639L, 12577890L, 12757260L,     12773671L, 12790422L, 12810198L, 12818524L, 12842341L, 12856710L,     12856793L, 12915159L, 12915739L, 12918073L, 12918160L, 12919494L,     12919845L, 12919898L, 13118253L, 13120501L, 13160080L, 13282838L,     13282983L, 13285623L, 13286659L, 13286792L, 13286877L, 13286962L,     13287020L, 13287222L, 13287387L, 13287472L, 13289113L, 13323638L,     13323691L, 13324653L, 13350626L, 13359097L, 13464903L, 13635004L,     13704353L, 13718405L, 13819666L, 13819719L, 13985911L, 13986406L,     14056633L, 14133858L, 14313520L, 14314109L, 14315820L, 14511764L,     14588816L, 14597593L, 14639519L, 14907955L, 14940717L, 14940828L,     14940897L, 14940948L, 14941025L, 14941130L, 14941197L, 14941346L,     14941406L, 14941637L, 14941749L, 15259443L, 15291837L, 15434385L,     15435097L, 15513968L, 15537767L, 15835031L, 15882977L, 15896767L,     16100354L, 16203121L, 16382181L, 16493374L, 16504231L, 16694417L,     16831878L, 16835203L, 16977369L, 17186899L, 17349226L, 17580063L,     17580422L, 17592342L, 17610111L, 17610540L, 17610862L, 17610985L,     17611116L, 17611229L, 17611340L, 17611721L, 17611807L, 17611815L,     17611885L, 17612015L, 17612538L, 17612637L, 17612900L, 17614033L,     17614064L, 17756688L, 17757370L, 18148359L, 18148604L, 18148734L,     18149278L, 18291725L, 18291909L, 18291977L, 18292803L, 18293066L,     18293340L, 18293954L, 18294056L, 18294177L, 18294221L, 18294237L,     18294620L, 18294714L, 18294852L, 18294979L, 18295114L, 18295420L,     18295860L, 18313632L, 18325924L, 18990647L, 18990713L, 18990850L,     18990984L, 18991149L, 18991221L, 18991314L, 18991523L, 18991600L,     18991655L, 18991727L, 18991783L, 18991855L, 18991969L, 18992123L,     18992441L, 18992581L, 18992721L, 19276891L, 19419541L, 19421035L,     19707553L, 19707682L, 19919479L, 19986324L, 20006454L, 20355792L,     20582590L, 20643362L, 20646054L, 20647821L, 20648184L, 20648604L,     20649149L, 20649867L, 20649916L, 20650183L, 20651148L, 20651248L,     20651460L, 20902146L, 20906221L, 20906855L, 20907136L, 21042088L,     21408409L, 21408417L, 21572300L, 21646223L, 21675840L, 21857459L,     22774386L, 22943017L, 23341310L, 23462501L, 23808565L, 24142364L,     24142438L, 24155576L, 24156424L, 24160312L, 24161303L, 24170511L,     24170903L, 24172206L, 24172284L, 24175451L, 24175803L, 24176542L,     24176627L, 24177177L, 24180327L, 24181107L, 24181114L, 24181250L,     24181314L, 24181369L, 24181423L, 24181749L, 24204507L, 24207449L,     24207761L, 24207826L, 24207846L, 24207850L, 24207855L, 24207926L,     24207956L, 24208057L, 24208082L, 24208095L, 24208114L, 24209420L,     24209965L, 24213244L, 24214949L, 24215527L, 24270133L, 24275952L,     24275983L, 24276000L, 24276248L, 24276882L, 24277178L, 24277239L,     24277290L, 24277298L, 24280200L, 24305543L, 24305550L, 24305559L,     24362045L, 24362168L, 24362284L, 24362382L, 24408128L, 24428431L,     24576779L, 24951621L, 24956969L, 25093294L, 25241651L, 25307712L,     25307788L, 25307857L, 25307896L, 25307999L, 25364577L, 25392823L,     25392872L, 25392926L, 25393222L, 25393613L, 25393617L, 25393865L,     25394135L, 25394164L, 25455015L, 25455145L, 25456851L, 25460137L,     25460528L, 25460666L, 25461996L, 25462078L, 25462194L, 25462252L,     25462296L, 25462304L, 25462367L, 25462465L, 25462660L, 25465564L,     25488356L, 25488695L, 25488763L, 25488795L, 25488868L, 25488890L,     25488991L, 25489018L, 25489031L, 25489049L, 25489080L, 25489094L,     25490897L, 25493483L, 25493539L, 25494303L, 25494660L, 25497847L,     25497898L, 25499200L, 25499592L, 25508820L, 25512302L, 25513687L,     25527658L, 25783770L, 25861487L, 25918431L, 26208087L, 26328981L,     26337463L, 26348502L, 26404401L, 26515656L, 26526600L, 26527618L,     26527674L, 26534432L, 26535380L, 26535387L, 26536179L, 26536473L,     26536906L, 26536913L, 26537117L, 26549860L, 26579722L, 26586313L,     26586722L, 26587405L, 26589544L, 26589603L, 26589920L, 26590261L,     26590421L, 26590509L, 26590669L, 26590821L, 26591156L, 26591380L,     26591534L, 26591693L, 26591753L, 26591815L, 26591900L, 26592218L,     26592472L, 26592616L, 26592745L, 26592826L, 26592908L, 26593012L,     26593178L, 26593283L, 26593354L, 26593741L, 26593984L, 26594111L,     26594293L, 26594396L, 26594557L, 26594996L, 26614511L, 26614548L,     26614779L, 26626808L, 26626971L), width = c(36L, 24L, 25L,     38L, 22L, 30L, 34L, 51L, 42L, 40L, 39L, 42L, 34L, 38L, 2L,     16L, 50L, 20L, 29L, 37L, 16L, 40L, 38L, 73L, 22L, 37L, 11L,     37L, 34L, 87L, 22L, 27L, 74L, 31L, 37L, 50L, 9L, 21L, 36L,     82L, 43L, 47L, 37L, 49L, 45L, 58L, 29L, 1L, 5L, 63L, 6L,     5L, 12L, 2L, 1L, 1L, 29L, 12L, 7L, 1L, 6L, 26L, 2L, 20L,     72L, 3L, 1L, 27L, 30L, 54L, 39L, 39L, 46L, 177L, 47L, 38L,     38L, 75L, 108L, 40L, 36L, 71L, 96L, 41L, 59L, 71L, 86L, 59L,     121L, 43L, 67L, 37L, 67L, 50L, 47L, 47L, 57L, 41L, 38L, 36L,     81L, 63L, 70L, 36L, 45L, 86L, 29L, 40L, 10L, 40L, 39L, 27L,     66L, 31L, 58L, 24L, 23L, 59L, 34L, 31L, 25L, 46L, 81L, 28L,     8L, 98L, 33L, 22L, 20L, 35L, 22L, 62L, 25L, 61L, 45L, 57L,     10L, 4L, 116L, 50L, 2L, 52L, 6L, 39L, 28L, 36L, 63L, 31L,     23L, 33L, 5L, 1L, 35L, 36L, 49L, 37L, 51L, 36L, 33L, 36L,     66L, 38L, 1L, 19L, 30L, 31L, 41L, 29L, 8L, 25L, 25L, 25L,     20L, 8L, 82L, 64L, 5L, 36L, 21L, 99L, 56L, 51L, 41L, 10L,     34L, 109L, 84L, 1L, 74L, 87L, 95L, 49L, 3L, 26L, 41L, 119L,     3L, 1L, 24L, 34L, 46L, 30L, 29L, 29L, 37L, 19L, 24L, 22L,     26L, 28L, 28L, 31L, 15L, 26L, 34L, 5L, 85L, 14L, 2L, 2L,     5L, 8L, 3L, 2L, 23L, 44L, 37L, 84L, 66L, 32L, 46L, 44L, 45L,     31L, 41L, 45L, 31L, 44L, 1L, 61L, 12L, 12L, 5L, 4L, 36L,     45L, 53L, 13L, 2L, 2L, 1L, 95L, 35L, 114L, 138L, 36L, 100L,     187L, 151L, 64L, 31L, 12L, 30L, 22L, 2L, 33L, 9L, 2L, 39L,     41L, 27L, 22L, 152L, 8L, 3L, 52L, 1L, 2L, 25L, 12L, 42L,     36L, 36L, 97L, 74L, 1L, 17L, 36L, 156L, 5L, 14L, 22L, 56L,     22L, 1L, 52L, 1L, 3L, 1L, 5L, 98L, 18L, 36L, 35L, 19L, 3L,     111L, 10L, 24L, 22L, 44L, 10L, 4L, 4L, 27L, 30L, 2L, 1L,     10L, 1L, 14L, 1L, 2L, 1L, 8L, 25L, 7L, 1L, 4L, 6L, 1L, 3L,     13L, 1L, 7L, 10L, 14L, 23L, 29L, 1L, 4L, 5L, 11L, 1L, 5L,     2L, 2L, 8L, 30L, 50L, 26L, 3L, 3L, 5L, 3L, 27L, 2L, 4L, 24L,     30L, 26L, 1L, 50L, 36L, 1L, 42L, 13L, 55L, 7L, 1L, 25L, 1L,     71L, 3L, 3L, 2L, 3L, 23L, 55L, 36L, 36L, 4L, 1L, 16L, 6L,     40L, 44L, 1L, 32L, 2L, 5L, 38L, 1L, 103L, 9L, 62L, 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25489099L, 25490915L,         25493518L, 25493607L, 25494339L, 25494699L, 25497872L,         25497933L, 25499242L, 25499634L, 25508833L, 25512336L,         25513723L, 25527701L, 25783787L, 25861524L, 25918466L,         26208113L, 26328985L, 26337473L, 26348521L, 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", 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       26590261L, 26590421L, 26590509L, 26590669L, 26590821L,         26591156L, 26591380L, 26591534L, 26591693L, 26591753L,         26591815L, 26591900L, 26592218L, 26592472L, 26592616L,         26592745L, 26592826L, 26592908L, 26593012L, 26593178L,         26593283L, 26593354L, 26593741L, 26593984L, 26594111L,         26594293L, 26594396L, 26594557L, 26594996L, 26614511L,         26614548L, 26614779L, 26626808L, 26626971L), indexEnd = c(2929829L,         2956701L, 2977227L, 2977994L, 2978871L, 2979033L, 2979110L,         2979231L, 2979870L, 2979952L, 2995015L, 2995144L, 2995273L,         2997511L, 2997681L, 3071378L, 3137095L, 3549339L, 3549410L,         3549545L, 3549668L, 3549722L, 3549912L, 3550041L, 3583423L,         3622433L, 3682797L, 3682917L, 3683061L, 3683425L, 3683476L,         3683579L, 3683704L, 3683968L, 3684087L, 3684337L, 3684462L,         3685965L, 3864675L, 3864853L, 3865449L, 3865577L, 3865675L,         3866002L, 3866066L, 3866670L, 3966387L, 4036399L, 4042451L,         4044271L, 4044278L, 4044327L, 4044340L, 4044496L, 4044498L,         4044500L, 4044530L, 4044617L, 4045051L, 4045056L, 4045072L,         4046173L, 4046176L, 4217730L, 4344851L, 4356018L, 4356021L,         4360809L, 4801125L, 5206558L, 5206675L, 5206829L, 5206901L,         5207301L, 5207365L, 5207529L, 5207625L, 5207835L, 5207955L,         5337651L, 5337766L, 5337883L, 5337980L, 5338139L, 5338200L,         5338293L, 5338409L, 5338546L, 5338715L, 5338826L, 5338895L,         5338941L, 5573256L, 5573508L, 5573583L, 5573647L, 5573718L,         5573823L, 5573870L, 5573908L, 5574100L, 5574374L, 5574478L,         5634625L, 5793319L, 5793478L, 5793658L, 5793750L, 5815563L,         5888018L, 6124459L, 6142036L, 6719031L, 6893764L, 6901235L,         6901349L, 6949120L, 7070782L, 7080089L, 7080817L, 7107149L,         7133958L, 7304025L, 7304093L, 7326169L, 7341212L, 7356184L,         7371855L, 7372755L, 7372826L, 7373060L, 7373213L, 7374622L,         7375777L, 7378389L, 7378498L, 7378509L, 7378516L, 7378634L,         7378731L, 7378919L, 7379968L, 7380059L, 7380194L, 7380547L,         7380642L, 7380746L, 7381087L, 7381345L, 7501949L, 7621337L,         7621353L, 7666382L, 8538316L, 8539010L, 8543615L, 8648171L,         8650111L, 8717704L, 8871329L, 9141961L, 9187807L, 9560331L,         9560354L, 9671927L, 9988268L, 10088100L, 10091525L, 10094663L,         10173682L, 10190490L, 10190643L, 10190846L, 10191525L,         10191805L, 10192086L, 10195470L, 10195948L, 10196275L,         10197377L, 10197520L, 10197823L, 10197879L, 10197890L,         10198161L, 10198328L, 10198487L, 10198489L, 10198571L,         10198667L, 10198799L, 10198885L, 10198889L, 10198979L,         10199065L, 10200282L, 10667003L, 10667011L, 10774060L,         10776411L, 10796143L, 10796350L, 10799307L, 10801662L,         10808038L, 10863083L, 10874678L, 10967562L, 10973618L,         10976935L, 10983080L, 10991247L, 10999930L, 11006922L,         11023305L, 11031609L, 11110816L, 11113991L, 11113995L,         11121716L, 11121870L, 11121881L, 11121890L, 11123707L,         11124305L, 11127346L, 11134838L, 11144384L, 11153881L,         11153982L, 11154110L, 11154185L, 11154413L, 11154516L,         11154694L, 11154740L, 11154817L, 11154965L, 11155227L,         11155289L, 11155302L, 11155328L, 11155408L, 11155414L,         11155451L, 11155779L, 11155884L, 11157201L, 11161917L,         11161927L, 11161930L, 11162036L, 11162102L, 11162229L,         11162409L, 11162492L, 11162630L, 11162861L, 11163057L,         11163139L, 11163218L, 11163873L, 11164024L, 11164704L,         11164734L, 11164768L, 11165210L, 11165217L, 11165445L,         11165800L, 11166029L, 11166087L, 11166361L, 11166418L,         11166472L, 11166657L, 11166686L, 11166689L, 11166718L,         11166732L, 11166779L, 11166887L, 11166999L, 11167128L,         11167234L, 11167268L, 11167291L, 11167356L, 11167526L,         11167590L, 11167609L, 11167702L, 11167892L, 11168091L,         11168095L, 11168278L, 11168289L, 11168299L, 11168301L,         11168307L, 11168462L, 11168629L, 11169498L, 11169550L,         11169901L, 11170045L, 11170157L, 11170312L, 11171074L,         11173458L, 11173614L, 11173727L, 11173732L, 11173747L,         11174488L, 11175804L, 11176263L, 11176265L, 11176389L,         11176391L, 11176408L, 11176410L, 11177652L, 11178128L,         11179575L, 11179603L, 11179684L, 11179688L, 11180032L,         11180423L, 11182918L, 11183388L, 11184235L, 11184436L,         11184893L, 11185263L, 11185278L, 11185903L, 11186140L,         11186454L, 11186463L, 11186471L, 11186602L, 11188462L,         11189537L, 11189544L, 11189552L, 11189561L, 11189641L,         11189801L, 11190500L, 11191256L, 11191265L, 11191922L,         11191932L, 11196440L, 11196444L, 11197336L, 11197615L,         11199159L, 11200312L, 11200412L, 11200735L, 11201489L,         11201700L, 11202740L, 11203066L, 11203381L, 11203392L,         11203400L, 11203435L, 11203442L, 11203535L, 11203539L,         11203599L, 11203613L, 11203632L, 11203745L, 11203922L,         11204126L, 11204191L, 11204233L, 11204242L, 11204483L,         11204492L, 11205055L, 11205124L, 11205279L, 11205312L,         11205316L, 11205524L, 11205737L, 11205753L, 11206247L,         11206258L, 11206323L, 11206452L, 11206641L, 11208224L,         11209289L, 11209720L, 11212482L, 11212802L, 11214307L,         11214975L, 11298868L, 11301496L, 11302755L, 11302757L,         11302793L, 11303125L, 11338072L, 11417445L, 11502609L,         11722039L, 11734890L, 11747728L, 11790858L, 11886830L,         11923572L, 12148280L, 12149661L, 12149967L, 12150288L,         12152619L, 12163962L, 12245324L, 12318978L, 12319678L,         12322618L, 12322833L, 12323065L, 12375489L, 12375501L,         12473458L, 12567503L, 12577677L, 12577945L, 12757295L,         12773703L, 12790464L, 12810240L, 12818561L, 12842369L,         12856716L, 12856837L, 12915214L, 12915774L, 12918114L,         12918185L, 12919530L, 12919878L, 12919971L, 13118297L,         13120534L, 13160108L, 13282872L, 13283018L, 13285658L,         13286767L, 13286838L, 13286959L, 13287016L, 13287088L,         13287350L, 13287440L, 13287533L, 13289146L, 13323678L,         13323722L, 13324695L, 13350684L, 13359132L, 13464941L,         13635010L, 13704400L, 13718430L, 13819702L, 13819758L,         13986094L, 13986433L, 14056819L, 14133902L, 14313556L,         14314109L, 14315834L, 14511792L, 14588841L, 14597626L,         14639547L, 14907999L, 14940754L, 14940875L, 14940929L,         14941002L, 14941122L, 14941171L, 14941315L, 14941384L,         14941475L, 14941684L, 14941786L, 15259478L, 15291869L,         15434392L, 15435128L, 15513996L, 15537780L, 15835054L,         15883024L, 15896816L, 16100366L, 16203160L, 16382216L,         16493395L, 16504262L, 16694452L, 16831914L, 16835231L,         16977370L, 17186921L, 17349252L, 17580083L, 17580447L,         17592375L, 17610149L, 17610595L, 17610895L, 17611034L,         17611157L, 17611297L, 17611386L, 17611779L, 17611813L,         17611821L, 17611951L, 17612056L, 17612559L, 17612667L,         17612955L, 17614060L, 17614099L, 17756731L, 17757405L,         18148384L, 18148639L, 18148750L, 18149321L, 18291752L,         18291972L, 18291978L, 18292830L, 18293109L, 18293375L,         18293994L, 18294135L, 18294214L, 18294221L, 18294290L,         18294670L, 18294781L, 18294893L, 18295024L, 18295147L,         18295463L, 18295898L, 18313663L, 18325944L, 18990708L,         18990759L, 18990974L, 18991077L, 18991193L, 18991275L,         18991378L, 18991569L, 18991650L, 18991717L, 18991776L,         18991847L, 18991954L, 18992110L, 18992432L, 18992569L,         18992675L, 18992798L, 19276928L, 19419576L, 19421069L,         19707586L, 19707727L, 19919514L, 19986361L, 20006458L,         20355826L, 20582626L, 20643400L, 20646092L, 20647866L,         20648223L, 20648651L, 20649173L, 20649867L, 20649971L,         20650229L, 20651193L, 20651298L, 20651506L, 20902171L,         20906251L, 20906895L, 20907171L, 21042123L, 21408415L,         21408418L, 21572334L, 21646242L, 21675877L, 21857493L,         22774410L, 22943045L, 23341323L, 23462518L, 23808602L,         24142374L, 24142477L, 24155578L, 24156454L, 24160319L,         24161327L, 24170554L, 24170943L, 24172235L, 24172298L,         24175476L, 24175835L, 24176609L, 24176662L, 24177204L,         24180355L, 24181110L, 24181149L, 24181277L, 24181365L,         24181388L, 24181458L, 24181782L, 24204541L, 24207486L,         24207771L, 24207836L, 24207846L, 24207851L, 24207890L,         24207951L, 24207958L, 24208079L, 24208082L, 24208105L,         24208126L, 24209471L, 24210006L, 24213293L, 24214992L,         24215549L, 24270151L, 24275981L, 24275987L, 24276009L,         24276282L, 24276936L, 24277222L, 24277277L, 24277292L,         24277309L, 24280206L, 24305546L, 24305555L, 24305561L,         24362141L, 24362281L, 24362361L, 24362432L, 24408153L,         24428463L, 24576795L, 24951649L, 24956975L, 25093322L,         25241682L, 25307756L, 25307854L, 25307892L, 25307971L,         25308093L, 25364602L, 25392857L, 25392909L, 25392970L,         25393268L, 25393614L, 25393637L, 25393899L, 25394150L,         25394199L, 25455050L, 25455192L, 25456889L, 25460175L,         25460548L, 25460718L, 25461996L, 25462117L, 25462226L,         25462292L, 25462297L, 25462335L, 25462387L, 25462483L,         25462694L, 25465633L, 25488391L, 25488718L, 25488770L,         25488825L, 25488887L, 25488897L, 25489014L, 25489018L,         25489033L, 25489051L, 25489084L, 25489099L, 25490915L,         25493518L, 25493607L, 25494339L, 25494699L, 25497872L,         25497933L, 25499242L, 25499634L, 25508833L, 25512336L,         25513723L, 25527701L, 25783787L, 25861524L, 25918466L,         26208113L, 26328985L, 26337473L, 26348521L, 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)),     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 ...