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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ExpressionNormalizationWorkflow
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* checking for file ‘ExpressionNormalizationWorkflow/DESCRIPTION’ ... OK
* preparing ‘ExpressionNormalizationWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 2017 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpRKH3V7/xshell33b305656c7' 2>&1
ERROR
--- re-building ‘genExpNrm.Rmd’ using rmarkdown
*** caught segfault ***
address 0x0, 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(0L, 5L, 6L, 8L, 10L, 0L, 5L, 6L, 8L, 10L, 0L, 3L, 6L, 9L, 10L, 0L, 3L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 8L, 11L, 2L, 5L, 6L, 9L, 10L, 0L, 4L, 6L, 9L, 10L, 0L, 5L, 6L, 8L, 11L, 0L, 4L, 6L, 9L, 10L, 0L, 5L, 6L, 8L, 10L, 2L, 5L, 6L, 8L, 11L, 0L, 5L, 6L, 9L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 5L, 6L, 8L, 10L, 2L, 4L, 6L, 9L, 10L, 0L, 4L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 3L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 1L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 11L, 2L, 3L, 6L, 8L, 11L, 1L, 5L, 6L, 9L, 11L, 1L, 5L, 6L, 8L, 11L, 0L, 5L, 6L, 8L, 11L, 1L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 11L, 0L, 5L, 6L, 9L, 11L, 0L, 4L, 6L, 9L, 10L, 1L, 3L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 10L, 0L, 4L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 10L, 0L, 4L, 6L, 8L, 10L, 0L, 4L, 6L, 9L, 10L, 2L, 3L, 6L, 8L, 11L, 0L, 5L, 6L, 9L, 11L, 0L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 10L, 0L, 3L, 6L, 8L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 4L, 7L, 8L, 11L, 0L, 5L, 7L, 9L, 11L, 2L, 3L, 7L, 8L, 10L, 1L, 5L, 7L, 8L, 10L, 1L, 5L, 7L, 9L, 10L, 1L, 3L, 7L, 9L, 10L, 1L, 5L, 7L, 8L, 10L, 1L, 5L, 7L, 9L, 10L, 2L, 3L, 7L, 9L, 10L, 1L, 5L, 7L, 9L, 10L, 2L, 5L, 7L, 9L, 11L, 1L, 3L, 7L, 9L, 11L, 2L, 5L, 7L, 9L, 11L, 1L, 4L, 7L, 9L, 11L, 1L, 3L, 7L, 9L, 10L, 1L, 5L, 7L, 8L, 10L, 1L, 4L, 7L, 9L, 10L, 2L, 5L, 7L, 9L, 10L, 2L, 3L, 7L, 8L, 10L, 1L, 4L, 7L, 9L, 10L, 1L, 5L, 7L, 9L, 10L, 1L, 5L, 7L, 9L, 11L, 1L, 5L, 7L, 9L, 11L, 1L, 5L, 7L, 9L, 11L, 2L, 5L, 7L, 9L, 11L, 2L, 5L, 7L, 8L, 11L, 0L, 4L, 7L, 9L, 11L, 0L, 5L, 7L, 8L, 11L, 1L, 4L, 7L, 8L, 11L, 0L, 4L, 7L, 8L, 11L, 1L, 3L, 7L, 8L, 11L, 2L, 5L, 7L, 9L, 11L, 2L, 3L, 7L, 9L, 10L, 1L, 3L, 7L, 9L, 10L, 1L, 3L, 7L, 8L, 11L, 2L, 5L, 7L, 9L, 10L, 2L, 4L, 7L, 8L, 11L, 2L, 5L, 7L, 9L, 10L, 2L, 5L, 7L, 9L, 11L, 2L, 3L, 7L, 9L, 10L, 1L, 3L, 7L, 8L, 10L, 2L, 3L, 7L, 9L, 10L, 2L, 3L, 7L, 9L, 11L, 0L, 4L, 7L, 9L, 10L, 1L, 5L, 7L, 8L, 11L, 0L, 3L, 7L, 9L, 11L, 0L, 3L, 7L, 9L, 11L, 2L, 5L, 7L, 9L, 11L, 1L, 4L, 7L, 9L, 10L), p = c(0L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 105L, 110L, 115L, 120L, 125L, 130L, 135L, 140L, 145L, 150L, 155L, 160L, 165L, 170L, 175L, 180L, 185L, 190L, 195L, 200L, 205L, 210L, 215L, 220L, 225L, 230L, 235L, 240L, 245L, 250L, 255L, 260L, 265L, 270L, 275L, 280L, 285L, 290L, 295L, 300L, 305L, 310L, 315L, 320L, 325L, 330L, 335L, 340L, 345L, 350L, 355L, 360L, 365L, 370L, 375L, 380L, 385L, 390L, 395L, 400L, 405L, 410L, 415L, 420L, 425L, 430L, 435L, 440L, 445L, 450L, 455L, 460L, 465L, 470L, 475L, 480L, 485L, 490L, 495L, 500L), Dim = c(12L, 100L), Dimnames = list(c("HIGH", "LOW", "MOD", "NORM", "OBESE", "OVER", "A", "B", "FEM", "MAL", "ACUTE", "FINE"), c("A001", "A002", "A003", "A004", "A005", "A006", "A007", "A008", "A009", "A010", "A011", "A012", "A013", "A014", "A015", "A016", "A017", "A018", "A019", "A020", "A021", "A022", "A023", "A024", "A025", "A026", "A027", "A028", "A029", "A030", "A031", "A032", "A033", "A034", "A035", "A036", "A037", "A038", "A039", "A040", "A041", "A042", "A043", "A044", "A045", "A046", "A047", "A048", "A049", "A050", "A051", "B052", "B053", "B054", "B055", "B056", "B057", "B058", "B059", "B060", "B061", "B062", "B063", "B064", "B065", "B066", "B067", "B068", "B069", "B070", "B071", "B072", "B073", "B074", "B075", "B076", "B077", "B078", "B079", "B080", "B081", "B082", "B083", "B084", "B085", "B086", "B087", "B088", "B089", "B090", "B091", "B092", "B093", "B094", "B095", "B096", "B097", "B098", "B099", "B100")), 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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), Lambdat = new("dgCMatrix", i = 0:11, p = 0:12, Dim = c(12L, 12L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L), n = 100L, 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))
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(-0.138051206600068, -0.077588350865412, -0.157558022296594, -0.15599959158715, 0.0288482859845001, -0.15349965268524, -0.00883095094736341, -0.0720353844685033, -0.0281380823993135, -0.00879542479069924, -0.00075444881687154, -0.048769182257558, -0.0122307512424864, -0.024694524054413, -0.0382537479068878, -0.0301154068118882, -0.120947223871385, -0.0639902086154552, -0.102278901065973, -0.132364913869504, -0.0984713088138583, -0.112603590178416, -0.0436927627322571, -0.0191032896706233, -0.0415808458144293, -0.0499960908226138, -0.0230116195623425, -0.127156526308692, -0.0522213285330688, 0.00694453168697598, -0.141718055596425, -0.107355409832, -0.0638195963154588, -0.141698851305825, -0.152320929229665, -0.0999990581074471, -0.031040059852392, -0.139263467070501, -0.00881919946693215, -0.103550482549292, -0.106457741776052, -0.0747387863668623, -0.0921935990506407, -0.143774908741499, -0.135986175732501, -0.114614999382158, -0.0627404021506006, -0.0636488788400331, -0.138481512292147, -0.153200486214618, -0.114373088680941, 0.048082898750698, 0.112103367920254, 0.140507643887708, 0.154735500445551, 0.0767948662993921, 0.11360584102092, 0.0797889860285033, 0.119023116038527, 0.140237719438086, 0.119761581550374, 0.0886524539287842, 0.116712272885354, 0.098481037006488, 0.100197698191079, 0.109418302202704, 0.151473807747067, 0.0428791197975458, 0.0871207593566502, 0.147665346690569, 0.0552216792653325, 0.119771850213634, 0.109412845879632, 0.0462608357448498, -0.0442739046157176, 0.0912610481009069, 0.0650735596674675, 0.00360404235585173, 0.101275284792387, 0.0899478462602219, 0.0338568350974885, 0.0565244181163742, 0.14940417268813, 0.118047500187136, 0.039542096243366, 0.0254179755091939, 0.136438405201423, 0.10207620805352, 0.110874610730787, 0.160518071600779, 0.103046854698162, 0.110420424606973, 0.121337311776837, 0.140045026552238, 0.0548515913210846, 0.0814044418881015, 0.151306334899137, 0.0580232972519429, 0.12551770812739, 0.103639832758529), CAD = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L), BMI3 = c(3L, 3L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 2L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 1L, 1L, 1L, 3L, 1L, 3L, 1L, 3L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 1L, 3L, 2L, 3L, 3L, 2L, 2L, 1L, 3L, 3L, 3L, 1L, 3L, 1L, 2L, 3L, 1L, 3L, 3L, 1L, 3L, 3L, 1L, 3L, 3L, 1L, 3L, 2L, 1L, 3L, 2L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 2L, 2L, 1L, 3L, 1L, 1L, 1L, 3L, 2L, 3L, 3L, 1L, 1L, 1L, 1L, 2L, 3L, 1L, 1L, 3L, 2L), Rin3 = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 3L, 1L, 3L, 3L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 3L, 2L, 2L, 1L, 2L, 3L, 1L, 1L, 2L, 3L, 1L, 1L, 3L, 1L, 1L, 3L, 1L, 1L, 3L, 1L, 3L, 3L, 3L, 1L, 3L, 2L, 2L, 2L, 2L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 2L, 2L, 2L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 3L, 2L), Gender = c(1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L), Study = c(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, 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, 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, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L)), 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), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 5L, 6L, 8L, 10L, 0L, 5L, 6L, 8L, 10L, 0L, 3L, 6L, 9L, 10L, 0L, 3L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 0L, 5L, 6L, 8L, 11L, 2L, 5L, 6L, 9L, 10L, 0L, 4L, 6L, 9L, 10L, 0L, 5L, 6L, 8L, 11L, 0L, 4L, 6L, 9L, 10L, 0L, 5L, 6L, 8L, 10L, 2L, 5L, 6L, 8L, 11L, 0L, 5L, 6L, 9L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 5L, 6L, 8L, 10L, 2L, 4L, 6L, 9L, 10L, 0L, 4L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 3L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 1L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 11L, 2L, 3L, 6L, 8L, 11L, 1L, 5L, 6L, 9L, 11L, 1L, 5L, 6L, 8L, 11L, 0L, 5L, 6L, 8L, 11L, 1L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 11L, 0L, 5L, 6L, 9L, 11L, 0L, 4L, 6L, 9L, 10L, 1L, 3L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 10L, 0L, 4L, 6L, 9L, 10L, 0L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 10L, 0L, 4L, 6L, 8L, 10L, 0L, 4L, 6L, 9L, 10L, 2L, 3L, 6L, 8L, 11L, 0L, 5L, 6L, 9L, 11L, 0L, 5L, 6L, 9L, 10L, 2L, 5L, 6L, 9L, 10L, 0L, 3L, 6L, 8L, 11L, 2L, 5L, 6L, 8L, 11L, 2L, 3L, 6L, 9L, 11L, 2L, 4L, 7L, 8L, 11L, 0L, 5L, 7L, 9L, 11L, 2L, 3L, 7L, 8L, 10L, 1L, 5L, 7L, 8L, 10L, 1L, 5L, 7L, 9L, 10L, 1L, 3L, 7L, 9L, 10L, 1L, 5L, 7L, 8L, 10L, 1L, 5L, 7L, 9L, 10L, 2L, 3L, 7L, 9L, 10L, 1L, 5L, 7L, 9L, 10L, 2L, 5L, 7L, 9L, 11L, 1L, 3L, 7L, 9L, 11L, 2L, 5L, 7L, 9L, 11L, 1L, 4L, 7L, 9L, 11L, 1L, 3L, 7L, 9L, 10L, 1L, 5L, 7L, 8L, 10L, 1L, 4L, 7L, 9L, 10L, 2L, 5L, 7L, 9L, 10L, 2L, 3L, 7L, 8L, 10L, 1L, 4L, 7L, 9L, 10L, 1L, 5L, 7L, 9L, 10L, 1L, 5L, 7L, 9L, 11L, 1L, 5L, 7L, 9L, 11L, 1L, 5L, 7L, 9L, 11L, 2L, 5L, 7L, 9L, 11L, 2L, 5L, 7L, 8L, 11L, 0L, 4L, 7L, 9L, 11L, 0L, 5L, 7L, 8L, 11L, 1L, 4L, 7L, 8L, 11L, 0L, 4L, 7L, 8L, 11L, 1L, 3L, 7L, 8L, 11L, 2L, 5L, 7L, 9L, 11L, 2L, 3L, 7L, 9L, 10L, 1L, 3L, 7L, 9L, 10L, 1L, 3L, 7L, 8L, 11L, 2L, 5L, 7L, 9L, 10L, 2L, 4L, 7L, 8L, 11L, 2L, 5L, 7L, 9L, 10L, 2L, 5L, 7L, 9L, 11L, 2L, 3L, 7L, 9L, 10L, 1L, 3L, 7L, 8L, 10L, 2L, 3L, 7L, 9L, 10L, 2L, 3L, 7L, 9L, 11L, 0L, 4L, 7L, 9L, 10L, 1L, 5L, 7L, 8L, 11L, 0L, 3L, 7L, 9L, 11L, 0L, 3L, 7L, 9L, 11L, 2L, 5L, 7L, 9L, 11L, 1L, 4L, 7L, 9L, 10L), p = c(0L, 5L, 10L, 15L, 20L, 25L, 30L, 35L, 40L, 45L, 50L, 55L, 60L, 65L, 70L, 75L, 80L, 85L, 90L, 95L, 100L, 105L, 110L, 115L, 120L, 125L, 130L, 135L, 140L, 145L, 150L, 155L, 160L, 165L, 170L, 175L, 180L, 185L, 190L, 195L, 200L, 205L, 210L, 215L, 220L, 225L, 230L, 235L, 240L, 245L, 250L, 255L, 260L, 265L, 270L, 275L, 280L, 285L, 290L, 295L, 300L, 305L, 310L, 315L, 320L, 325L, 330L, 335L, 340L, 345L, 350L, 355L, 360L, 365L, 370L, 375L, 380L, 385L, 390L, 395L, 400L, 405L, 410L, 415L, 420L, 425L, 430L, 435L, 440L, 445L, 450L, 455L, 460L, 465L, 470L, 475L, 480L, 485L, 490L, 495L, 500L), Dim = c(12L, 100L), Dimnames = list( c("HIGH", "LOW", "MOD", "NORM", "OBESE", "OVER", "A", "B", "FEM", "MAL", "ACUTE", "FINE"), c("A001", "A002", "A003", "A004", "A005", "A006", "A007", "A008", "A009", "A010", "A011", "A012", "A013", "A014", "A015", "A016", "A017", "A018", "A019", "A020", "A021", "A022", "A023", "A024", "A025", "A026", "A027", "A028", "A029", "A030", "A031", "A032", "A033", "A034", "A035", "A036", "A037", "A038", "A039", "A040", "A041", "A042", "A043", "A044", "A045", "A046", "A047", "A048", "A049", "A050", "A051", "B052", "B053", "B054", "B055", "B056", "B057", "B058", "B059", "B060", "B061", "B062", "B063", "B064", "B065", "B066", "B067", "B068", "B069", "B070", "B071", "B072", "B073", "B074", "B075", "B076", "B077", "B078", "B079", "B080", "B081", "B082", "B083", "B084", "B085", "B086", "B087", "B088", "B089", "B090", "B091", "B092", "B093", "B094", "B095", "B096", "B097", "B098", "B099", "B100")), 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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), Lind = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L), Gp = c(0L, 3L, 6L, 8L, 10L, 12L), lower = c(0, 0, 0, 0, 0), Lambdat = new("dgCMatrix", i = 0:11, p = 0:12, Dim = c(12L, 12L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), flist = list(Rin3 = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 3L, 1L, 3L, 3L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 3L, 2L, 2L, 1L, 2L, 3L, 1L, 1L, 2L, 3L, 1L, 1L, 3L, 1L, 1L, 3L, 1L, 1L, 3L, 1L, 3L, 3L, 3L, 1L, 3L, 2L, 2L, 2L, 2L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 2L, 2L, 2L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 3L, 3L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 3L, 2L), BMI3 = c(3L, 3L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 2L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 1L, 1L, 1L, 3L, 1L, 3L, 1L, 3L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 1L, 3L, 2L, 3L, 3L, 2L, 2L, 1L, 3L, 3L, 3L, 1L, 3L, 1L, 2L, 3L, 1L, 3L, 3L, 1L, 3L, 3L, 1L, 3L, 3L, 1L, 3L, 2L, 1L, 3L, 2L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 2L, 2L, 1L, 3L, 1L, 1L, 1L, 3L, 2L, 3L, 3L, 1L, 1L, 1L, 1L, 2L, 3L, 1L, 1L, 3L, 2L), Study = c(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, 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, 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, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), Gender = c(1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L), CAD = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L)), cnms = list( Rin3 = "(Intercept)", BMI3 = "(Intercept)", Study = "(Intercept)", Gender = "(Intercept)", CAD = "(Intercept)"), Ztlist = list( `1 | Rin3` = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 0L, 0L, 0L, 0L, 2L, 0L, 2L, 2L, 2L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 0L, 1L, 2L, 0L, 0L, 1L, 2L, 0L, 0L, 2L, 0L, 0L, 2L, 0L, 0L, 2L, 0L, 2L, 2L, 2L, 0L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 0L, 0L, 1L, 0L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 0L, 1L, 0L, 0L, 2L, 1L), p = 0:100, Dim = c(3L, 100L), Dimnames = list(c("HIGH", "LOW", "MOD"), c("A001", "A002", "A003", "A004", "A005", "A006", "A007", "A008", "A009", "A010", "A011", "A012", "A013", "A014", "A015", "A016", "A017", "A018", "A019", "A020", "A021", "A022", "A023", "A024", "A025", "A026", "A027", "A028", "A029", "A030", "A031", "A032", "A033", "A034", "A035", "A036", "A037", "A038", "A039", "A040", "A041", "A042", "A043", "A044", "A045", "A046", "A047", "A048", "A049", "A050", "A051", "B052", "B053", "B054", "B055", "B056", "B057", "B058", "B059", "B060", "B061", "B062", "B063", "B064", "B065", "B066", "B067", "B068", "B069", "B070", "B071", "B072", "B073", "B074", "B075", "B076", "B077", "B078", "B079", "B080", "B081", "B082", "B083", "B084", "B085", "B086", "B087", "B088", "B089", "B090", "B091", "B092", "B093", "B094", "B095", "B096", "B097", "B098", "B099", "B100")), 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), factors = list()), `1 | BMI3` = new("dgCMatrix", i = c(2L, 2L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 0L, 0L, 0L, 2L, 0L, 2L, 0L, 2L, 2L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 0L, 2L, 1L, 2L, 2L, 1L, 1L, 0L, 2L, 2L, 2L, 0L, 2L, 0L, 1L, 2L, 0L, 2L, 2L, 0L, 2L, 2L, 0L, 2L, 2L, 0L, 2L, 1L, 0L, 2L, 1L, 2L, 0L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 0L, 2L, 0L, 0L, 0L, 2L, 1L, 2L, 2L, 0L, 0L, 0L, 0L, 1L, 2L, 0L, 0L, 2L, 1L), p = 0:100, Dim = c(3L, 100L), Dimnames = list(c("NORM", "OBESE", "OVER" ), c("A001", "A002", "A003", "A004", "A005", "A006", "A007", "A008", "A009", "A010", "A011", "A012", "A013", "A014", "A015", "A016", "A017", "A018", "A019", "A020", "A021", "A022", "A023", "A024", "A025", "A026", "A027", "A028", "A029", "A030", "A031", "A032", "A033", "A034", "A035", "A036", "A037", "A038", "A039", "A040", "A041", "A042", "A043", "A044", "A045", "A046", "A047", "A048", "A049", "A050", "A051", "B052", "B053", "B054", "B055", "B056", "B057", "B058", "B059", "B060", "B061", "B062", "B063", "B064", "B065", "B066", "B067", "B068", "B069", "B070", "B071", "B072", "B073", "B074", "B075", "B076", "B077", "B078", "B079", "B080", "B081", "B082", "B083", "B084", "B085", "B086", "B087", "B088", "B089", "B090", "B091", "B092", "B093", "B094", "B095", "B096", "B097", "B098", "B099", "B100")), 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), factors = list()), `1 | Study` = new("dgCMatrix", i = c(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, 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, 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), p = 0:100, Dim = c(2L, 100L ), Dimnames = list(c("A", "B"), c("A001", "A002", "A003", "A004", "A005", "A006", "A007", "A008", "A009", "A010", "A011", "A012", "A013", "A014", "A015", "A016", "A017", "A018", "A019", "A020", "A021", "A022", "A023", "A024", "A025", "A026", "A027", "A028", "A029", "A030", "A031", "A032", "A033", "A034", "A035", "A036", "A037", "A038", "A039", "A040", "A041", "A042", "A043", "A044", "A045", "A046", "A047", "A048", "A049", "A050", "A051", "B052", "B053", "B054", "B055", "B056", "B057", "B058", "B059", "B060", "B061", "B062", "B063", "B064", "B065", "B066", "B067", "B068", "B069", "B070", "B071", "B072", "B073", "B074", "B075", "B076", "B077", "B078", "B079", "B080", "B081", "B082", "B083", "B084", "B085", "B086", "B087", "B088", "B089", "B090", "B091", "B092", "B093", "B094", "B095", "B096", "B097", "B098", "B099", "B100" )), 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), factors = list()), `1 | Gender` = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L), p = 0:100, Dim = c(2L, 100L), Dimnames = list(c("FEM", "MAL"), c("A001", "A002", "A003", "A004", "A005", "A006", "A007", "A008", "A009", "A010", "A011", "A012", "A013", "A014", "A015", "A016", "A017", "A018", "A019", "A020", "A021", "A022", "A023", "A024", "A025", "A026", "A027", "A028", "A029", "A030", "A031", "A032", "A033", "A034", "A035", "A036", "A037", "A038", "A039", "A040", "A041", "A042", "A043", "A044", "A045", "A046", "A047", "A048", "A049", "A050", "A051", "B052", "B053", "B054", "B055", "B056", "B057", "B058", "B059", "B060", "B061", "B062", "B063", "B064", "B065", "B066", "B067", "B068", "B069", "B070", "B071", "B072", "B073", "B074", "B075", "B076", "B077", "B078", "B079", "B080", "B081", "B082", "B083", "B084", "B085", "B086", "B087", "B088", "B089", "B090", "B091", "B092", "B093", "B094", "B095", "B096", "B097", "B098", "B099", "B100")), 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), factors = list()), `1 | CAD` = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 1L, 0L), p = 0:100, Dim = c(2L, 100L), Dimnames = list(c("ACUTE", "FINE"), c("A001", "A002", "A003", "A004", "A005", "A006", "A007", "A008", "A009", "A010", "A011", "A012", "A013", "A014", "A015", "A016", "A017", "A018", "A019", "A020", "A021", "A022", "A023", "A024", "A025", "A026", "A027", "A028", "A029", "A030", "A031", "A032", "A033", "A034", "A035", "A036", "A037", "A038", "A039", "A040", "A041", "A042", "A043", "A044", "A045", "A046", "A047", "A048", "A049", "A050", "A051", "B052", "B053", "B054", "B055", "B056", "B057", "B058", "B059", "B060", "B061", "B062", "B063", "B064", "B065", "B066", "B067", "B068", "B069", "B070", "B071", "B072", "B073", "B074", "B075", "B076", "B077", "B078", "B079", "B080", "B081", "B082", "B083", "B084", "B085", "B086", "B087", "B088", "B089", "B090", "B091", "B092", "B093", "B094", "B095", "B096", "B097", "B098", "B099", "B100")), 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), factors = list())), nl = c(Rin3 = 3L, BMI3 = 3L, Study = 2L, Gender = 2L, CAD = 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(exp_datObj, batch_factors, pct_threshold)
13: pvcAnaly(inpData, pct_thrsh, cvrts_eff_var)
14: eval(expr, envir, enclos)
15: eval(expr, envir, enclos)
16: eval_with_user_handlers(expr, envir, enclos, user_handlers)
17: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
18: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
19: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
21: 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, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
22: evaluate::evaluate(...)
23: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
24: in_dir(input_dir(), expr)
25: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
26: eng_r(options)
27: block_exec(params)
28: call_block(x)
29: process_group.block(group)
30: process_group(group)
31: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
32: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
33: handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
34: process_file(text, output)
35: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
36: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
37: vweave_rmarkdown(...)
38: engine$weave(file, quiet = quiet, encoding = enc)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, classes, parentenv, handlers)
42: 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)))})
43: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...