This page was generated on 2024-03-28 11:39:39 -0400 (Thu, 28 Mar 2024).
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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 MSstatsTMT
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* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* preparing ‘MSstatsTMT’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 16958 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpEhcuHh/xshell3ee87ef1e7fb' 2>&1
ERROR
--- re-building ‘MSstatsTMT.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, 20L, 35L, 2L, 20L, 35L, 3L, 20L, 35L, 1L, 20L, 35L, 1L, 20L, 35L, 0L, 20L, 35L, 2L, 20L, 35L, 3L, 20L, 35L, 0L, 21L, 35L, 2L, 21L, 35L, 3L, 21L, 35L, 1L, 21L, 35L, 1L, 21L, 35L, 0L, 21L, 35L, 2L, 21L, 35L, 3L, 21L, 35L, 0L, 22L, 35L, 2L, 22L, 35L, 3L, 22L, 35L, 1L, 22L, 35L, 1L, 22L, 35L, 0L, 22L, 35L, 2L, 22L, 35L, 3L, 22L, 35L, 7L, 23L, 36L, 5L, 23L, 36L, 4L, 23L, 36L, 6L, 23L, 36L, 6L, 23L, 36L, 7L, 23L, 36L, 5L, 23L, 36L, 4L, 23L, 36L, 7L, 24L, 36L, 5L, 24L, 36L, 4L, 24L, 36L, 6L, 24L, 36L, 6L, 24L, 36L, 7L, 24L, 36L, 5L, 24L, 36L, 4L, 24L, 36L, 7L, 25L, 36L, 5L, 25L, 36L, 4L, 25L, 36L, 6L, 25L, 36L, 6L, 25L, 36L, 7L, 25L, 36L, 5L, 25L, 36L, 4L, 25L, 36L, 10L, 26L, 37L, 8L, 26L, 37L, 9L, 26L, 37L, 11L, 26L, 37L, 8L, 26L, 37L, 9L, 26L, 37L, 11L, 26L, 37L, 10L, 26L, 37L, 10L, 27L, 37L, 8L, 27L, 37L, 9L, 27L, 37L, 11L, 27L, 37L, 8L, 27L, 37L, 9L, 27L, 37L, 11L, 27L, 37L, 10L, 27L, 37L, 10L, 28L, 37L, 8L, 28L, 37L, 9L, 28L, 37L, 11L, 28L, 37L, 8L, 28L, 37L, 9L, 28L, 37L, 11L, 28L, 37L, 10L, 28L, 37L, 13L, 29L, 38L, 15L, 29L, 38L, 14L, 29L, 38L, 12L, 29L, 38L, 15L, 29L, 38L, 14L, 29L, 38L, 12L, 29L, 38L, 13L, 29L, 38L, 13L, 30L, 38L, 15L, 30L, 38L, 14L, 30L, 38L, 12L, 30L, 38L, 15L, 30L, 38L, 14L, 30L, 38L, 12L, 30L, 38L, 13L, 30L, 38L, 13L, 31L, 38L, 15L, 31L, 38L, 14L, 31L, 38L, 12L, 31L, 38L, 15L, 31L, 38L, 14L, 31L, 38L, 12L, 31L, 38L, 13L, 31L, 38L, 16L, 32L, 39L, 18L, 32L, 39L, 19L, 32L, 39L, 17L, 32L, 39L, 17L, 32L, 39L, 16L, 32L, 39L, 18L, 32L, 39L, 19L, 32L, 39L, 16L, 33L, 39L, 18L, 33L, 39L, 19L, 33L, 39L, 17L, 33L, 39L, 17L, 33L, 39L, 16L, 33L, 39L, 18L, 33L, 39L, 19L, 33L, 39L, 16L, 34L, 39L, 18L, 34L, 39L, 19L, 34L, 39L, 17L, 34L, 39L, 17L, 34L, 39L, 16L, 34L, 39L, 18L, 34L, 39L, 19L, 34L, 39L), p = c(0L, 3L, 6L, 9L, 12L, 15L, 18L, 21L, 24L, 27L, 30L, 33L, 36L, 39L, 42L, 45L, 48L, 51L, 54L, 57L, 60L, 63L, 66L, 69L, 72L, 75L, 78L, 81L, 84L, 87L, 90L, 93L, 96L, 99L, 102L, 105L, 108L, 111L, 114L, 117L, 120L, 123L, 126L, 129L, 132L, 135L, 138L, 141L, 144L, 147L, 150L, 153L, 156L, 159L, 162L, 165L, 168L, 171L, 174L, 177L, 180L, 183L, 186L, 189L, 192L, 195L, 198L, 201L, 204L, 207L, 210L, 213L, 216L, 219L, 222L, 225L, 228L, 231L, 234L, 237L, 240L, 243L, 246L, 249L, 252L, 255L, 258L, 261L, 264L, 267L, 270L, 273L, 276L, 279L, 282L, 285L, 288L, 291L, 294L, 297L, 300L, 303L, 306L, 309L, 312L, 315L, 318L, 321L, 324L, 327L, 330L, 333L, 336L, 339L, 342L, 345L, 348L, 351L, 354L, 357L, 360L), Dim = c(40L, 120L), Dimnames = list(c("Mixture1_0.125", "Mixture1_0.5", "Mixture1_0.667", "Mixture1_1", "Mixture2_0.125", "Mixture2_0.5", "Mixture2_0.667", "Mixture2_1", "Mixture3_0.125", "Mixture3_0.5", "Mixture3_0.667", "Mixture3_1", "Mixture4_0.125", "Mixture4_0.5", "Mixture4_0.667", "Mixture4_1", "Mixture5_0.125", "Mixture5_0.5", "Mixture5_0.667", "Mixture5_1", "Mixture1:1", "Mixture1:2", "Mixture1:3", "Mixture2:1", "Mixture2:2", "Mixture2:3", "Mixture3:1", "Mixture3:2", "Mixture3:3", "Mixture4:1", "Mixture4:2", "Mixture4:3", "Mixture5:1", "Mixture5:2", "Mixture5:3", "Mixture1", "Mixture2", "Mixture3", "Mixture4", "Mixture5"), c("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", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120")), 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), factors = list()), theta = c(1, 1, 1), Lambdat = new("dgCMatrix", i = 0:39, p = 0:40, Dim = c(40L, 40L), 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, 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, 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, 3L, 3L, 3L, 3L, 3L), n = 120L, 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, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 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(Abundance = c(16.5981240067408, 16.5110582757449, 16.6517685351404, 16.7178298762783, 16.6719046124296, 16.5572887988767, 16.494481730482, 16.6595231832318, 16.5278476533993, 16.6087548745279, 16.6422215742024, 16.5060909262532, 16.6478017789209, 16.4859712533246, 16.5479137252186, 16.6135118193593, 16.597922048877, 16.5437863811447, 16.6318588123051, 16.5768081631917, 16.5126402401422, 16.6127211961285, 16.6474086709374, 16.583178602372, 16.7072343432572, 16.640280461957, 16.5351365875751, 16.6565836832881, 16.5568728240573, 16.6158576864981, 16.5433807013869, 16.5909893871506, 16.6237946798194, 16.6538993081779, 16.45604334395, 16.6419846925685, 16.6974332360658, 16.5755924183203, 16.6517145483469, 16.4306776611365, 16.594258141957, 16.680224905867, 16.7021224838771, 16.6972066363189, 16.6675786125849, 16.7271104729405, 16.6971595682434, 16.5998832169083, 16.5836484383228, 16.6198839813992, 16.6370877849492, 16.6187051113009, 16.6269697900013, 16.4158308286411, 16.2140570807683, 16.5557248064919, 16.4459874714479, 16.5561450962302, 16.5574567707276, 16.50296992997, 16.5710677831739, 16.5015888144652, 16.5403262023258, 16.5750269862666, 16.5264750853648, 16.6157176141321, 16.6472171002085, 16.6927892507181, 16.4201340034736, 16.6166905987261, 16.6420660882917, 16.6286682583759, 16.5984045114515, 16.503829765825, 16.4377447765499, 16.6352276913071, 16.5483502874874, 16.6192617162842, 16.5665881549071, 16.4823172143412, 16.4693261264621, 16.456885370227, 16.5003598314818, 16.4604219122362, 16.4235297682871, 16.310170865932, 16.2869816032604, 16.3583498143705, 16.462030373532, 16.342129324012, 16.6151149442133, 16.5464714350061, 16.5581975137967, 16.5954201283941, 16.4550549627702, 16.6579984406959, 16.5450715491084, 16.5437282336074, 16.6884949000644, 16.6095057233993, 16.5393404103124, 16.5968288887794, 16.588025281256, 16.4611023658489, 16.5901870831502, 16.6137583025933, 16.4938674923723, 16.5689565829522, 16.6460317667733, 16.6684208074425, 16.6019174846236, 16.4488410611863, 16.9037507327187, 16.6262849328484, 16.7253399217754, 16.7696641758872, 16.9684414668737, 16.705104264302, 16.7396594090209, 16.7549937788123), Mixture = 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, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 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, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), TechRepMixture = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), Group = c(1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 4L, 2L, 1L, 3L, 3L, 4L, 2L, 1L, 4L, 2L, 1L, 3L, 3L, 4L, 2L, 1L, 4L, 2L, 1L, 3L, 3L, 4L, 2L, 1L, 3L, 1L, 2L, 4L, 1L, 2L, 4L, 3L, 3L, 1L, 2L, 4L, 1L, 2L, 4L, 3L, 3L, 1L, 2L, 4L, 1L, 2L, 4L, 3L, 2L, 4L, 3L, 1L, 4L, 3L, 1L, 2L, 2L, 4L, 3L, 1L, 4L, 3L, 1L, 2L, 2L, 4L, 3L, 1L, 4L, 3L, 1L, 2L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L), Subject = c(1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 8L, 6L, 5L, 7L, 7L, 8L, 6L, 5L, 8L, 6L, 5L, 7L, 7L, 8L, 6L, 5L, 8L, 6L, 5L, 7L, 7L, 8L, 6L, 5L, 11L, 9L, 10L, 12L, 9L, 10L, 12L, 11L, 11L, 9L, 10L, 12L, 9L, 10L, 12L, 11L, 11L, 9L, 10L, 12L, 9L, 10L, 12L, 11L, 14L, 16L, 15L, 13L, 16L, 15L, 13L, 14L, 14L, 16L, 15L, 13L, 16L, 15L, 13L, 14L, 14L, 16L, 15L, 13L, 16L, 15L, 13L, 14L, 17L, 19L, 20L, 18L, 18L, 17L, 19L, 20L, 17L, 19L, 20L, 18L, 18L, 17L, 19L, 20L, 17L, 19L, 20L, 18L, 18L, 17L, 19L, 20L)), 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, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 20L, 35L, 2L, 20L, 35L, 3L, 20L, 35L, 1L, 20L, 35L, 1L, 20L, 35L, 0L, 20L, 35L, 2L, 20L, 35L, 3L, 20L, 35L, 0L, 21L, 35L, 2L, 21L, 35L, 3L, 21L, 35L, 1L, 21L, 35L, 1L, 21L, 35L, 0L, 21L, 35L, 2L, 21L, 35L, 3L, 21L, 35L, 0L, 22L, 35L, 2L, 22L, 35L, 3L, 22L, 35L, 1L, 22L, 35L, 1L, 22L, 35L, 0L, 22L, 35L, 2L, 22L, 35L, 3L, 22L, 35L, 7L, 23L, 36L, 5L, 23L, 36L, 4L, 23L, 36L, 6L, 23L, 36L, 6L, 23L, 36L, 7L, 23L, 36L, 5L, 23L, 36L, 4L, 23L, 36L, 7L, 24L, 36L, 5L, 24L, 36L, 4L, 24L, 36L, 6L, 24L, 36L, 6L, 24L, 36L, 7L, 24L, 36L, 5L, 24L, 36L, 4L, 24L, 36L, 7L, 25L, 36L, 5L, 25L, 36L, 4L, 25L, 36L, 6L, 25L, 36L, 6L, 25L, 36L, 7L, 25L, 36L, 5L, 25L, 36L, 4L, 25L, 36L, 10L, 26L, 37L, 8L, 26L, 37L, 9L, 26L, 37L, 11L, 26L, 37L, 8L, 26L, 37L, 9L, 26L, 37L, 11L, 26L, 37L, 10L, 26L, 37L, 10L, 27L, 37L, 8L, 27L, 37L, 9L, 27L, 37L, 11L, 27L, 37L, 8L, 27L, 37L, 9L, 27L, 37L, 11L, 27L, 37L, 10L, 27L, 37L, 10L, 28L, 37L, 8L, 28L, 37L, 9L, 28L, 37L, 11L, 28L, 37L, 8L, 28L, 37L, 9L, 28L, 37L, 11L, 28L, 37L, 10L, 28L, 37L, 13L, 29L, 38L, 15L, 29L, 38L, 14L, 29L, 38L, 12L, 29L, 38L, 15L, 29L, 38L, 14L, 29L, 38L, 12L, 29L, 38L, 13L, 29L, 38L, 13L, 30L, 38L, 15L, 30L, 38L, 14L, 30L, 38L, 12L, 30L, 38L, 15L, 30L, 38L, 14L, 30L, 38L, 12L, 30L, 38L, 13L, 30L, 38L, 13L, 31L, 38L, 15L, 31L, 38L, 14L, 31L, 38L, 12L, 31L, 38L, 15L, 31L, 38L, 14L, 31L, 38L, 12L, 31L, 38L, 13L, 31L, 38L, 16L, 32L, 39L, 18L, 32L, 39L, 19L, 32L, 39L, 17L, 32L, 39L, 17L, 32L, 39L, 16L, 32L, 39L, 18L, 32L, 39L, 19L, 32L, 39L, 16L, 33L, 39L, 18L, 33L, 39L, 19L, 33L, 39L, 17L, 33L, 39L, 17L, 33L, 39L, 16L, 33L, 39L, 18L, 33L, 39L, 19L, 33L, 39L, 16L, 34L, 39L, 18L, 34L, 39L, 19L, 34L, 39L, 17L, 34L, 39L, 17L, 34L, 39L, 16L, 34L, 39L, 18L, 34L, 39L, 19L, 34L, 39L), p = c(0L, 3L, 6L, 9L, 12L, 15L, 18L, 21L, 24L, 27L, 30L, 33L, 36L, 39L, 42L, 45L, 48L, 51L, 54L, 57L, 60L, 63L, 66L, 69L, 72L, 75L, 78L, 81L, 84L, 87L, 90L, 93L, 96L, 99L, 102L, 105L, 108L, 111L, 114L, 117L, 120L, 123L, 126L, 129L, 132L, 135L, 138L, 141L, 144L, 147L, 150L, 153L, 156L, 159L, 162L, 165L, 168L, 171L, 174L, 177L, 180L, 183L, 186L, 189L, 192L, 195L, 198L, 201L, 204L, 207L, 210L, 213L, 216L, 219L, 222L, 225L, 228L, 231L, 234L, 237L, 240L, 243L, 246L, 249L, 252L, 255L, 258L, 261L, 264L, 267L, 270L, 273L, 276L, 279L, 282L, 285L, 288L, 291L, 294L, 297L, 300L, 303L, 306L, 309L, 312L, 315L, 318L, 321L, 324L, 327L, 330L, 333L, 336L, 339L, 342L, 345L, 348L, 351L, 354L, 357L, 360L), Dim = c(40L, 120L), Dimnames = list(c("Mixture1_0.125", "Mixture1_0.5", "Mixture1_0.667", "Mixture1_1", "Mixture2_0.125", "Mixture2_0.5", "Mixture2_0.667", "Mixture2_1", "Mixture3_0.125", "Mixture3_0.5", "Mixture3_0.667", "Mixture3_1", "Mixture4_0.125", "Mixture4_0.5", "Mixture4_0.667", "Mixture4_1", "Mixture5_0.125", "Mixture5_0.5", "Mixture5_0.667", "Mixture5_1", "Mixture1:1", "Mixture1:2", "Mixture1:3", "Mixture2:1", "Mixture2:2", "Mixture2:3", "Mixture3:1", "Mixture3:2", "Mixture3:3", "Mixture4:1", "Mixture4:2", "Mixture4:3", "Mixture5:1", "Mixture5:2", "Mixture5:3", "Mixture1", "Mixture2", "Mixture3", "Mixture4", "Mixture5"), c("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", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120")), 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), factors = list()), theta = c(1, 1, 1), Lind = 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, 2L, 3L, 3L, 3L, 3L, 3L), Gp = c(0L, 20L, 35L, 40L), lower = c(0, 0, 0 ), Lambdat = new("dgCMatrix", i = 0:39, p = 0:40, Dim = c(40L, 40L), 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), flist = list(Subject = c(1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 1L, 3L, 4L, 2L, 2L, 1L, 3L, 4L, 8L, 6L, 5L, 7L, 7L, 8L, 6L, 5L, 8L, 6L, 5L, 7L, 7L, 8L, 6L, 5L, 8L, 6L, 5L, 7L, 7L, 8L, 6L, 5L, 11L, 9L, 10L, 12L, 9L, 10L, 12L, 11L, 11L, 9L, 10L, 12L, 9L, 10L, 12L, 11L, 11L, 9L, 10L, 12L, 9L, 10L, 12L, 11L, 14L, 16L, 15L, 13L, 16L, 15L, 13L, 14L, 14L, 16L, 15L, 13L, 16L, 15L, 13L, 14L, 14L, 16L, 15L, 13L, 16L, 15L, 13L, 14L, 17L, 19L, 20L, 18L, 18L, 17L, 19L, 20L, 17L, 19L, 20L, 18L, 18L, 17L, 19L, 20L, 17L, 19L, 20L, 18L, 18L, 17L, 19L, 20L), `Mixture:TechRepMixture` = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L), Mixture = 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, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 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, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L)), cnms = list(Subject = "(Intercept)", `Mixture:TechRepMixture` = "(Intercept)", Mixture = "(Intercept)"), Ztlist = list(`1 | Subject` = new("dgCMatrix", i = c(0L, 2L, 3L, 1L, 1L, 0L, 2L, 3L, 0L, 2L, 3L, 1L, 1L, 0L, 2L, 3L, 0L, 2L, 3L, 1L, 1L, 0L, 2L, 3L, 7L, 5L, 4L, 6L, 6L, 7L, 5L, 4L, 7L, 5L, 4L, 6L, 6L, 7L, 5L, 4L, 7L, 5L, 4L, 6L, 6L, 7L, 5L, 4L, 10L, 8L, 9L, 11L, 8L, 9L, 11L, 10L, 10L, 8L, 9L, 11L, 8L, 9L, 11L, 10L, 10L, 8L, 9L, 11L, 8L, 9L, 11L, 10L, 13L, 15L, 14L, 12L, 15L, 14L, 12L, 13L, 13L, 15L, 14L, 12L, 15L, 14L, 12L, 13L, 13L, 15L, 14L, 12L, 15L, 14L, 12L, 13L, 16L, 18L, 19L, 17L, 17L, 16L, 18L, 19L, 16L, 18L, 19L, 17L, 17L, 16L, 18L, 19L, 16L, 18L, 19L, 17L, 17L, 16L, 18L, 19L), p = 0:120, Dim = c(20L, 120L), Dimnames = list(c("Mixture1_0.125", "Mixture1_0.5", "Mixture1_0.667", "Mixture1_1", "Mixture2_0.125", "Mixture2_0.5", "Mixture2_0.667", "Mixture2_1", "Mixture3_0.125", "Mixture3_0.5", "Mixture3_0.667", "Mixture3_1", "Mixture4_0.125", "Mixture4_0.5", "Mixture4_0.667", "Mixture4_1", "Mixture5_0.125", "Mixture5_0.5", "Mixture5_0.667", "Mixture5_1"), c("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", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120")), 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), factors = list()), `1 | Mixture:TechRepMixture` = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L), p = 0:120, Dim = c(15L, 120L), Dimnames = list(c("Mixture1:1", "Mixture1:2", "Mixture1:3", "Mixture2:1", "Mixture2:2", "Mixture2:3", "Mixture3:1", "Mixture3:2", "Mixture3:3", "Mixture4:1", "Mixture4:2", "Mixture4:3", "Mixture5:1", "Mixture5:2", "Mixture5:3"), c("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", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120")), 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), factors = list()), `1 | Mixture` = 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, 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, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), p = 0:120, Dim = c(5L, 120L), Dimnames = list( c("Mixture1", "Mixture2", "Mixture3", "Mixture4", "Mixture5"), c("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", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120")), 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), factors = list())), nl = c(Subject = 20L, `Mixture:TechRepMixture` = 15L, Mixture = 5L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L, 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: lme4::lmer(formula = Abundance ~ 1 + (1 | Mixture) + (1 | Mixture:TechRepMixture) + Group + (1 | Subject), data = data)
12: eval(expr, p)
13: eval(expr, p)
14: eval.parent(mc)
15: lmerTest::lmer(Abundance ~ 1 + (1 | Mixture) + (1 | Mixture:TechRepMixture) + Group + (1 | Subject), data = data)
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(lmerTest::lmer(Abundance ~ 1 + (1 | Mixture) + (1 | Mixture:TechRepMixture) + Group + (1 | Subject), data = data), TRUE)
21: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
22: suppressMessages(try(lmerTest::lmer(Abundance ~ 1 + (1 | Mixture) + (1 | Mixture:TechRepMixture) + Group + (1 | Subject), data = data), TRUE))
23: fit_Mix_TechRep_Group_Sub_model(single_protein)
24: .fitModelTMT(single_protein, has_single_subject, has_techreps, has_biomixtures, has_single_run, has_Repeated_Measures)
25: MSstatsComparisonModelSingleTMT(single_protein, protein)
26: MSstatsFitComparisonModelsTMT(summarized)
27: groupComparisonTMT(quant.msstats, moderated = TRUE)
28: eval(expr, envir, enclos)
29: eval(expr, envir, enclos)
30: eval_with_user_handlers(expr, envir, enclos, user_handlers)
31: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
32: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
33: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
34: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
35: 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)
36: evaluate::evaluate(...)
37: 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$render, options))
38: in_dir(input_dir(), expr)
39: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
40: eng_r(options)
41: block_exec(params)
42: call_block(x)
43: process_group.block(group)
44: process_group(group)
45: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
46: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
47: handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
48: process_file(text, output)
49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
51: vweave_rmarkdown(...)
52: engine$weave(file, quiet = quiet, encoding = enc)
53: doTryCatch(return(expr), name, parentenv, handler)
54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
55: tryCatchList(expr, classes, parentenv, handlers)
56: 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)))})
57: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...