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This page was generated on 2024-03-28 11:41:09 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1614/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pvca 1.43.0 (landing page) Jianying LI
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the pvca package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pvca.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: pvca |
Version: 1.43.0 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data pvca |
StartedAt: 2024-03-28 00:47:02 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 00:47:28 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 26.0 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data pvca ### ############################################################################## ############################################################################## * checking for file ‘pvca/DESCRIPTION’ ... OK * preparing ‘pvca’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘pvca.Rnw’ using Sweave Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. *** caught segfault *** address 0x40ff4000000000c4, cause 'memory not mapped' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$initialize(...) 4: initialize(value, ...) 5: initialize(value, ...) 6: methods::new(def, ...) 7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 3L, 8L, 12L, 19L, 20L, 22L, 3L, 8L, 12L, 19L, 20L, 22L, 3L, 8L, 12L, 19L, 20L, 22L, 4L, 9L, 15L, 16L, 21L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 1L, 10L, 14L, 17L, 20L, 23L, 1L, 10L, 14L, 17L, 20L, 23L, 5L, 10L, 15L, 17L, 21L, 23L, 5L, 10L, 15L, 17L, 21L, 23L, 5L, 10L, 15L, 17L, 21L, 23L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L), p = c(0L, 6L, 12L, 18L, 24L, 30L, 36L, 42L, 48L, 54L, 60L, 66L, 72L, 78L, 84L, 90L, 96L, 102L, 108L, 114L, 120L, 126L, 132L, 138L, 144L, 150L, 156L, 162L, 168L, 174L, 180L, 186L, 192L, 198L, 204L, 210L, 216L, 222L, 228L, 234L, 240L, 246L, 252L, 258L, 264L, 270L, 276L, 282L, 288L, 294L, 300L, 306L, 312L, 318L, 324L, 330L, 336L, 342L, 348L, 354L, 360L, 366L, 372L, 378L, 384L, 390L, 396L, 402L, 408L, 414L, 420L, 426L, 432L), Dim = c(24L, 72L), Dimnames = list(c("BM:CALGB", "BM:CCG", "BM:DFCI", "BM:St-Jude", "PB:CALGB", "PB:CCG", "PB:DFCI", "ALL:DFCI", "ALL:St-Jude", "AML:CALGB", "AML:CCG", "AML:St-Jude", "ALL:BM", "ALL:PB", "AML:BM", "AML:PB", "CALGB", "CCG", "DFCI", "St-Jude", "BM", "PB", "ALL", "AML"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = c(1, 1, 1, 1, 1, 1), Lambdat = new("dgCMatrix", i = 0:23, p = 0:24, Dim = c(24L, 24L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 6L, 6L), n = 72L, X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)) 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0, control = lmerControl(), ...) { p <- ncol(X) rho <- new.env(parent = parent.env(environment())) rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) REMLpass <- if (REML) p else 0L rho$resp <- if (missing(fr)) mkRespMod(REML = REMLpass, ...) else mkRespMod(fr, REML = REMLpass) pp <- resp <- NULL rho$lmer_Deviance <- lmer_Deviance devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(), resp$ptr(), as.double(theta)) environment(devfun) <- rho if (is.null(start) && all(reTrms$cnms == "(Intercept)") && length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) { v <- sapply(reTrms$flist, function(f) var(ave(y, f))) v.e <- var(y) - sum(v) if (!is.na(v.e) && v.e > 0) { v.rel <- v/v.e if (all(v.rel >= reTrms$lower^2)) rho$pp$setTheta(sqrt(v.rel)) } } if (length(rho$resp$y) > 0) devfun(rho$pp$theta) rho$lower <- reTrms$lower devfun})(fr = list(pc_data_matrix = c(-0.023440865842773, 0.0408654720597722, -0.0497154745514352, -0.116261020665713, -0.21608512928618, 0.0527119332893529, -0.184093688250068, -0.0748199999231626, -0.148038048641923, -0.110847609750701, -0.144426617461885, -0.0456315495767911, -0.0687790502042405, -0.100194125873401, -0.169702836228454, -0.206668431180158, -0.00655619594007762, -0.020581908657693, -0.0259618251591223, -0.0785826901208854, 0.0807407797110188, 0.154724817200358, 0.197678035506807, 0.188286010420154, 0.000173958230369008, 0.0834649043796893, 0.130419925888418, 0.0380034280428189, 0.0955135231984068, 0.12532538637552, -0.0670617459920365, 0.127380650113468, 0.112176304147893, 0.0872783430946773, -0.0474782980154908, 0.012798295094662, 0.0301905865170706, -0.0129412771590243, -0.189357374681198, 0.0449482582163091, 0.0465806884891742, 0.0680319387309288, -0.0346126830462741, 0.00261687433555754, -0.033772347184925, 0.0650378034322366, -0.244318998430324, -0.025320803787997, -0.222171521405384, -0.150532118693273, -0.0197321040783781, -0.0377573985409088, -0.132192878768104, -0.221684845010566, -0.0818512952332565, 0.0289417686628849, 0.0477158620389402, -0.152054420555118, -0.0183760598972864, -0.137956939184746, 0.0702046394723854, 0.157477214998023, 0.13557861139541, 0.157341085991551, 0.175864909101293, 0.123619829107737, 0.1158244416756, 0.0416563967465367, 0.138197909454589, 0.163194923869104, 0.131905549533244, 0.201833447556854), ALL.AML = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), BM.PB = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), Source = c(3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 4L, 4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), reTrms = list(Zt = new("dgCMatrix", i = c(2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 6L, 7L, 13L, 18L, 21L, 22L, 3L, 8L, 12L, 19L, 20L, 22L, 3L, 8L, 12L, 19L, 20L, 22L, 3L, 8L, 12L, 19L, 20L, 22L, 4L, 9L, 15L, 16L, 21L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 3L, 11L, 14L, 19L, 20L, 23L, 1L, 10L, 14L, 17L, 20L, 23L, 1L, 10L, 14L, 17L, 20L, 23L, 5L, 10L, 15L, 17L, 21L, 23L, 5L, 10L, 15L, 17L, 21L, 23L, 5L, 10L, 15L, 17L, 21L, 23L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 2L, 7L, 12L, 18L, 20L, 22L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L, 0L, 9L, 14L, 16L, 20L, 23L), p = c(0L, 6L, 12L, 18L, 24L, 30L, 36L, 42L, 48L, 54L, 60L, 66L, 72L, 78L, 84L, 90L, 96L, 102L, 108L, 114L, 120L, 126L, 132L, 138L, 144L, 150L, 156L, 162L, 168L, 174L, 180L, 186L, 192L, 198L, 204L, 210L, 216L, 222L, 228L, 234L, 240L, 246L, 252L, 258L, 264L, 270L, 276L, 282L, 288L, 294L, 300L, 306L, 312L, 318L, 324L, 330L, 336L, 342L, 348L, 354L, 360L, 366L, 372L, 378L, 384L, 390L, 396L, 402L, 408L, 414L, 420L, 426L, 432L), Dim = c(24L, 72L), Dimnames = list(c("BM:CALGB", "BM:CCG", "BM:DFCI", "BM:St-Jude", "PB:CALGB", "PB:CCG", "PB:DFCI", "ALL:DFCI", "ALL:St-Jude", "AML:CALGB", "AML:CCG", "AML:St-Jude", "ALL:BM", "ALL:PB", "AML:BM", "AML:PB", "CALGB", "CCG", "DFCI", "St-Jude", "BM", "PB", "ALL", "AML"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = c(1, 1, 1, 1, 1, 1), Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 6L, 6L), Gp = c(0L, 7L, 12L, 16L, 20L, 22L, 24L), lower = c(0, 0, 0, 0, 0, 0), Lambdat = new("dgCMatrix", i = 0:23, p = 0:24, Dim = c(24L, 24L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), flist = list( `BM.PB:Source` = c(3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 7L, 7L, 7L, 7L, 7L, 7L, 4L, 4L, 4L, 5L, 1L, 1L, 1L, 4L, 4L, 4L, 4L, 4L, 2L, 2L, 6L, 6L, 6L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), `ALL.AML:Source` = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), `ALL.AML:BM.PB` = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), Source = c(3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 4L, 4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L ), BM.PB = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), ALL.AML = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L)), cnms = list( `BM.PB:Source` = "(Intercept)", `ALL.AML:Source` = "(Intercept)", `ALL.AML:BM.PB` = "(Intercept)", Source = "(Intercept)", BM.PB = "(Intercept)", ALL.AML = "(Intercept)"), Ztlist = list( `1 | BM.PB:Source` = new("dgCMatrix", i = c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 6L, 6L, 6L, 6L, 6L, 6L, 3L, 3L, 3L, 4L, 0L, 0L, 0L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 5L, 5L, 5L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), p = 0:72, Dim = c(7L, 72L), Dimnames = list(c("BM:CALGB", "BM:CCG", "BM:DFCI", "BM:St-Jude", "PB:CALGB", "PB:CCG", "PB:DFCI"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), `1 | ALL.AML:Source` = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 4L, 4L, 4L, 4L, 4L, 3L, 3L, 3L, 3L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L ), p = 0:72, Dim = c(5L, 72L), Dimnames = list(c("ALL:DFCI", "ALL:St-Jude", "AML:CALGB", "AML:CCG", "AML:St-Jude"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33" )), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), `1 | ALL.AML:BM.PB` = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), p = 0:72, Dim = c(4L, 72L), Dimnames = list(c("ALL:BM", "ALL:PB", "AML:BM", "AML:PB"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), `1 | Source` = new("dgCMatrix", i = c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 0L, 0L, 0L, 0L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), p = 0:72, Dim = c(4L, 72L), Dimnames = list(c("CALGB", "CCG", "DFCI", "St-Jude"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), `1 | BM.PB` = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), p = 0:72, Dim = c(2L, 72L), Dimnames = list(c("BM", "PB"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), `1 | ALL.AML` = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), p = 0:72, Dim = c(2L, 72L), Dimnames = list(c("ALL", "AML"), c("39", "40", "42", "47", "48", "49", "41", "43", "44", "45", "46", "70", "71", "72", "68", "69", "67", "55", "56", "59", "52", "53", "51", "50", "54", "57", "58", "60", "61", "65", "66", "63", "64", "62", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "34", "35", "36", "37", "38", "28", "29", "30", "31", "32", "33")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list())), nl = c(`BM.PB:Source` = 7L, `ALL.AML:Source` = 5L, `ALL.AML:BM.PB` = 4L, Source = 4L, BM.PB = 2L, ALL.AML = 2L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = FALSE, control = list(optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", check.scaleX = "warning", check.formula.LHS = "stop"), checkConv = list(check.conv.grad = list( action = "warning", tol = 0.002, relTol = NULL), check.conv.singular = list(action = "message", tol = 1e-04), check.conv.hess = list(action = "warning", tol = 1e-06)), optCtrl = list())) 10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose, control = control))) 11: lmer(funct, Data[y:(((i - 1) * expDesignRowN) + expDesignRowN), ], REML = TRUE, verbose = FALSE, na.action = na.omit) 12: pvcaBatchAssess(Golub_Merge, batch.factors, pct_threshold) 13: eval(expr, .GlobalEnv) 14: eval(expr, .GlobalEnv) 15: withVisible(eval(expr, .GlobalEnv)) 16: doTryCatch(return(expr), name, parentenv, handler) 17: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 18: tryCatchList(expr, classes, parentenv, handlers) 19: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 20: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE) 21: evalFunc(ce, options) 22: tryCatchList(expr, classes, parentenv, handlers) 23: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()}) 24: driver$runcode(drobj, chunk, chunkopts) 25: utils::Sweave(...) 26: engine$weave(file, quiet = quiet, encoding = enc) 27: doTryCatch(return(expr), name, parentenv, handler) 28: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 29: tryCatchList(expr, classes, parentenv, handlers) 30: tryCatch({ engine$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)))}) 31: tools::buildVignettes(dir = ".", tangle = TRUE) An irrecoverable exception occurred. R is aborting now ...