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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data pvca
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* 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 (nil), cause 'unknown'
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(-0.0234408658427739, 0.0408654720597711, -0.0497154745514349, -0.116261020665713, -0.21608512928618, 0.0527119332893516, -0.184093688250069, -0.0748199999231618, -0.148038048641924, -0.110847609750702, -0.144426617461885, -0.0456315495767922, -0.0687790502042401, -0.100194125873401, -0.169702836228454, -0.206668431180157, -0.0065561959400767, -0.0205819086576927, -0.0259618251591223, -0.0785826901208848, 0.0807407797110197, 0.154724817200358, 0.197678035506807, 0.188286010420154, 0.000173958230370762, 0.0834649043796908, 0.130419925888419, 0.0380034280428201, 0.0955135231984072, 0.12532538637552, -0.067061745992036, 0.127380650113468, 0.112176304147893, 0.0872783430946784, -0.0474782980154922, 0.0127982950946618, 0.0301905865170689, -0.0129412771590261, -0.189357374681199, 0.0449482582163076, 0.0465806884891727, 0.0680319387309272, -0.0346126830462754, 0.00261687433555657, -0.033772347184926, 0.0650378034322354, -0.244318998430323, -0.0253208037879971, -0.222171521405384, -0.150532118693273, -0.0197321040783782, -0.0377573985409084, -0.132192878768104, -0.221684845010565, -0.0818512952332574, 0.0289417686628836, 0.0477158620389384, -0.152054420555117, -0.0183760598972866, -0.137956939184746, 0.0702046394723839, 0.157477214998023, 0.13557861139541, 0.157341085991553, 0.175864909101294, 0.123619829107737, 0.1158244416756, 0.0416563967465384, 0.13819790945459, 0.163194923869103, 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 ...
Segmentation fault (core dumped)
