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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 variancePartition
###
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* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* preparing ‘variancePartition’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: variancePartition
* saving partial Rd database
* creating vignettes ...sh: line 1: 76385 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmp31fQjI/xshell1261b244d329d' 2>&1
ERROR
--- re-building ‘FAQ.Rmd’ using rmarkdown
--- finished re-building ‘FAQ.Rmd’
--- re-building ‘additional_visualization.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, 25L, 1L, 27L, 2L, 27L, 3L, 25L, 4L, 25L, 5L, 26L, 6L, 25L, 7L, 25L, 8L, 26L, 9L, 26L, 10L, 27L, 11L, 25L, 12L, 25L, 13L, 26L, 14L, 26L, 15L, 27L, 16L, 27L, 17L, 25L, 18L, 25L, 19L, 27L, 20L, 27L, 21L, 27L, 22L, 27L, 23L, 26L, 24L, 26L, 0L, 25L, 1L, 26L, 2L, 27L, 3L, 26L, 4L, 27L, 5L, 26L, 6L, 27L, 7L, 25L, 8L, 26L, 9L, 26L, 10L, 27L, 11L, 27L, 12L, 25L, 13L, 25L, 14L, 25L, 15L, 26L, 16L, 26L, 17L, 25L, 18L, 27L, 19L, 26L, 20L, 26L, 21L, 25L, 22L, 25L, 23L, 27L, 24L, 26L, 0L, 25L, 1L, 26L, 2L, 27L, 3L, 26L, 4L, 27L, 5L, 26L, 6L, 26L, 7L, 27L, 8L, 25L, 9L, 25L, 10L, 26L, 11L, 25L, 12L, 26L, 13L, 25L, 14L, 25L, 15L, 25L, 16L, 26L, 17L, 27L, 18L, 26L, 19L, 26L, 20L, 27L, 21L, 26L, 22L, 27L, 23L, 27L, 24L, 26L, 0L, 25L, 1L, 26L, 2L, 27L, 3L, 26L, 4L, 26L, 5L, 25L, 6L, 26L, 7L, 27L, 8L, 26L, 9L, 25L, 10L, 26L, 11L, 27L, 12L, 27L, 13L, 25L, 14L, 25L, 15L, 26L, 16L, 27L, 17L, 27L, 18L, 25L, 19L, 27L, 20L, 27L, 21L, 27L, 22L, 25L, 23L, 26L, 24L, 25L), p = c(0L, 2L, 4L, 6L, 8L, 10L, 12L, 14L, 16L, 18L, 20L, 22L, 24L, 26L, 28L, 30L, 32L, 34L, 36L, 38L, 40L, 42L, 44L, 46L, 48L, 50L, 52L, 54L, 56L, 58L, 60L, 62L, 64L, 66L, 68L, 70L, 72L, 74L, 76L, 78L, 80L, 82L, 84L, 86L, 88L, 90L, 92L, 94L, 96L, 98L, 100L, 102L, 104L, 106L, 108L, 110L, 112L, 114L, 116L, 118L, 120L, 122L, 124L, 126L, 128L, 130L, 132L, 134L, 136L, 138L, 140L, 142L, 144L, 146L, 148L, 150L, 152L, 154L, 156L, 158L, 160L, 162L, 164L, 166L, 168L, 170L, 172L, 174L, 176L, 178L, 180L, 182L, 184L, 186L, 188L, 190L, 192L, 194L, 196L, 198L, 200L), Dim = c(28L, 100L), Dimnames = list(c("1", "5", "9", "13", "18", "22", "26", "30", "34", "38", "42", "46", "50", "55", "59", "63", "67", "71", "75", "79", "84", "88", "92", "96", "100", "A", "B", "C"), c("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20", "s21", "s22", "s23", "s24", "s25", "s26", "s27", "s28", "s29", "s30", "s31", "s32", "s33", "s34", "s35", "s36", "s37", "s38", "s39", "s40", "s41", "s42", "s43", "s44", "s45", "s46", "s47", "s48", "s49", "s50", "s51", "s52", "s53", "s54", "s55", "s56", "s57", "s58", "s59", "s60", "s61", "s62", "s63", "s64", "s65", "s66", "s67", "s68", "s69", "s70", "s71", "s72", "s73", "s74", "s75", "s76", "s77", "s78", "s79", "s80", "s81", "s82", "s83", "s84", "s85", "s86", "s87", "s88", "s89", "s90", "s91", "s92", "s93", "s94", "s95", "s96", "s97", "s98", "s99", "s100")), 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), factors = list()), theta = c(1, 1), Lambdat = new("dgCMatrix", i = 0:27, p = 0:28, Dim = c(28L, 28L), 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), factors = list()), Lind = 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, 2L, 2L, 2L), 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, 44, 42, 49, 48, 56, 43, 37, 48, 50, 56, 39, 60, 54, 57, 50, 51, 73, 44, 44, 68, 52, 49, 62, 40, 54, 39, 53, 45, 52, 61, 47, 52, 36, 58, 46, 58, 40, 48, 54, 66, 41, 46, 51, 53, 57, 47, 44, 52, 39, 39, 60, 56, 47, 57, 50, 38, 56, 52, 52, 67, 48, 57, 53, 42, 48, 60, 54, 48, 44, 50, 49, 53, 45, 46, 47, 44, 52, 48, 53, 61, 46, 48, 41, 51, 64, 40, 44, 51, 47, 52, 57, 50, 53, 48, 44, 41, 64, 48, 59, 47))
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(y.local = c(-2.33007892278791, -2.05785598059545, -1.88517703243204, -1.75530050130824, -1.64967267935348, -1.55977999210325, -1.48097265136818, -1.41041953133823, -1.34626266523192, -1.28721373281733, -1.23234086111175, -1.18094704079664, -1.13249652961897, -1.08656811498607, -1.04282423903843, -1.00098991688188, -0.960837931003161, -0.922178178277587, -0.884849841298243, -0.848715527422145, -0.813656808115194, -0.779570773738484, -0.746367337187046, -0.713967098197978, -0.682299633211387, -0.651302112261564, -0.620918170042296, -0.591096976572805, -0.561792466099252, -0.532962692534297, -0.504569286898186, -0.476576997588236, -0.448953298361999, -0.42166805201953, -0.394693220159391, -0.368002611239332, -0.341571660625871, -0.31537723746266, -0.289397474096462, -0.263611614524901, -0.237999878911871, -0.212543341685061, -0.187223821108856, -0.162023778532748, -0.13692622576425, -0.111914639216988, -0.0869728796474011, -0.062085116423953, -0.0372357553759338, -0.0124093693486799, 0.0124093693486799, 0.0372357553759338, 0.062085116423953, 0.0869728796474012, 0.111914639216988, 0.13692622576425, 0.162023778532748, 0.187223821108856, 0.212543341685061, 0.237999878911871, 0.263611614524901, 0.289397474096462, 0.31537723746266, 0.341571660625871, 0.368002611239332, 0.394693220159391, 0.421668052019531, 0.448953298361999, 0.476576997588236, 0.504569286898185, 0.532962692534297, 0.561792466099251, 0.591096976572805, 0.620918170042296, 0.651302112261564, 0.682299633211387, 0.713967098197978, 0.746367337187046, 0.779570773738484, 0.813656808115194, 0.848715527422145, 0.884849841298243, 0.922178178277587, 0.960837931003161, 1.00098991688188, 1.04282423903843, 1.08656811498607, 1.13249652961897, 1.18094704079664, 1.23234086111175, 1.28721373281733, 1.34626266523192, 1.41041953133824, 1.48097265136818, 1.55977999210325, 1.64967267935348, 1.75530050130824, 1.88517703243204, 2.05785598059545, 2.33007892278791), Age = c(44L, 42L, 49L, 48L, 56L, 43L, 37L, 48L, 50L, 56L, 39L, 60L, 54L, 57L, 50L, 51L, 73L, 44L, 44L, 68L, 52L, 49L, 62L, 40L, 54L, 39L, 53L, 45L, 52L, 61L, 47L, 52L, 36L, 58L, 46L, 58L, 40L, 48L, 54L, 66L, 41L, 46L, 51L, 53L, 57L, 47L, 44L, 52L, 39L, 39L, 60L, 56L, 47L, 57L, 50L, 38L, 56L, 52L, 52L, 67L, 48L, 57L, 53L, 42L, 48L, 60L, 54L, 48L, 44L, 50L, 49L, 53L, 45L, 46L, 47L, 44L, 52L, 48L, 53L, 61L, 46L, 48L, 41L, 51L, 64L, 40L, 44L, 51L, 47L, 52L, 57L, 50L, 53L, 48L, 44L, 41L, 64L, 48L, 59L, 47L), Individual = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L), Tissue = c(1L, 3L, 3L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 3L, 1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 3L, 3L, 3L, 3L, 2L, 2L, 1L, 2L, 3L, 2L, 3L, 2L, 3L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 1L, 3L, 2L, 2L, 1L, 1L, 3L, 2L, 1L, 2L, 3L, 2L, 3L, 2L, 2L, 3L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 3L, 2L, 2L, 3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 2L, 2L, 1L, 2L, 3L, 2L, 1L, 2L, 3L, 3L, 1L, 1L, 2L, 3L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L), `(weights)` = 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)), 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, 44, 42, 49, 48, 56, 43, 37, 48, 50, 56, 39, 60, 54, 57, 50, 51, 73, 44, 44, 68, 52, 49, 62, 40, 54, 39, 53, 45, 52, 61, 47, 52, 36, 58, 46, 58, 40, 48, 54, 66, 41, 46, 51, 53, 57, 47, 44, 52, 39, 39, 60, 56, 47, 57, 50, 38, 56, 52, 52, 67, 48, 57, 53, 42, 48, 60, 54, 48, 44, 50, 49, 53, 45, 46, 47, 44, 52, 48, 53, 61, 46, 48, 41, 51, 64, 40, 44, 51, 47, 52, 57, 50, 53, 48, 44, 41, 64, 48, 59, 47), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 25L, 1L, 27L, 2L, 27L, 3L, 25L, 4L, 25L, 5L, 26L, 6L, 25L, 7L, 25L, 8L, 26L, 9L, 26L, 10L, 27L, 11L, 25L, 12L, 25L, 13L, 26L, 14L, 26L, 15L, 27L, 16L, 27L, 17L, 25L, 18L, 25L, 19L, 27L, 20L, 27L, 21L, 27L, 22L, 27L, 23L, 26L, 24L, 26L, 0L, 25L, 1L, 26L, 2L, 27L, 3L, 26L, 4L, 27L, 5L, 26L, 6L, 27L, 7L, 25L, 8L, 26L, 9L, 26L, 10L, 27L, 11L, 27L, 12L, 25L, 13L, 25L, 14L, 25L, 15L, 26L, 16L, 26L, 17L, 25L, 18L, 27L, 19L, 26L, 20L, 26L, 21L, 25L, 22L, 25L, 23L, 27L, 24L, 26L, 0L, 25L, 1L, 26L, 2L, 27L, 3L, 26L, 4L, 27L, 5L, 26L, 6L, 26L, 7L, 27L, 8L, 25L, 9L, 25L, 10L, 26L, 11L, 25L, 12L, 26L, 13L, 25L, 14L, 25L, 15L, 25L, 16L, 26L, 17L, 27L, 18L, 26L, 19L, 26L, 20L, 27L, 21L, 26L, 22L, 27L, 23L, 27L, 24L, 26L, 0L, 25L, 1L, 26L, 2L, 27L, 3L, 26L, 4L, 26L, 5L, 25L, 6L, 26L, 7L, 27L, 8L, 26L, 9L, 25L, 10L, 26L, 11L, 27L, 12L, 27L, 13L, 25L, 14L, 25L, 15L, 26L, 16L, 27L, 17L, 27L, 18L, 25L, 19L, 27L, 20L, 27L, 21L, 27L, 22L, 25L, 23L, 26L, 24L, 25L), p = c(0L, 2L, 4L, 6L, 8L, 10L, 12L, 14L, 16L, 18L, 20L, 22L, 24L, 26L, 28L, 30L, 32L, 34L, 36L, 38L, 40L, 42L, 44L, 46L, 48L, 50L, 52L, 54L, 56L, 58L, 60L, 62L, 64L, 66L, 68L, 70L, 72L, 74L, 76L, 78L, 80L, 82L, 84L, 86L, 88L, 90L, 92L, 94L, 96L, 98L, 100L, 102L, 104L, 106L, 108L, 110L, 112L, 114L, 116L, 118L, 120L, 122L, 124L, 126L, 128L, 130L, 132L, 134L, 136L, 138L, 140L, 142L, 144L, 146L, 148L, 150L, 152L, 154L, 156L, 158L, 160L, 162L, 164L, 166L, 168L, 170L, 172L, 174L, 176L, 178L, 180L, 182L, 184L, 186L, 188L, 190L, 192L, 194L, 196L, 198L, 200L), Dim = c(28L, 100L), Dimnames = list( c("1", "5", "9", "13", "18", "22", "26", "30", "34", "38", "42", "46", "50", "55", "59", "63", "67", "71", "75", "79", "84", "88", "92", "96", "100", "A", "B", "C"), c("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20", "s21", "s22", "s23", "s24", "s25", "s26", "s27", "s28", "s29", "s30", "s31", "s32", "s33", "s34", "s35", "s36", "s37", "s38", "s39", "s40", "s41", "s42", "s43", "s44", "s45", "s46", "s47", "s48", "s49", "s50", "s51", "s52", "s53", "s54", "s55", "s56", "s57", "s58", "s59", "s60", "s61", "s62", "s63", "s64", "s65", "s66", "s67", "s68", "s69", "s70", "s71", "s72", "s73", "s74", "s75", "s76", "s77", "s78", "s79", "s80", "s81", "s82", "s83", "s84", "s85", "s86", "s87", "s88", "s89", "s90", "s91", "s92", "s93", "s94", "s95", "s96", "s97", "s98", "s99", "s100")), 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), factors = list()), theta = c(1, 1), Lind = 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, 2L, 2L, 2L), Gp = c(0L, 25L, 28L), lower = c(0, 0), Lambdat = new("dgCMatrix", i = 0:27, p = 0:28, Dim = c(28L, 28L), 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), factors = list()), flist = list( Individual = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L), Tissue = c(1L, 3L, 3L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 3L, 1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 3L, 3L, 3L, 3L, 2L, 2L, 1L, 2L, 3L, 2L, 3L, 2L, 3L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 1L, 3L, 2L, 2L, 1L, 1L, 3L, 2L, 1L, 2L, 3L, 2L, 3L, 2L, 2L, 3L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 3L, 2L, 2L, 3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 2L, 2L, 1L, 2L, 3L, 2L, 1L, 2L, 3L, 3L, 1L, 1L, 2L, 3L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L)), cnms = list(Individual = "(Intercept)", Tissue = "(Intercept)"), Ztlist = list(`1 | Individual` = new("dgCMatrix", i = c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L), p = 0:100, Dim = c(25L, 100L), Dimnames = list(c("1", "5", "9", "13", "18", "22", "26", "30", "34", "38", "42", "46", "50", "55", "59", "63", "67", "71", "75", "79", "84", "88", "92", "96", "100"), c("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20", "s21", "s22", "s23", "s24", "s25", "s26", "s27", "s28", "s29", "s30", "s31", "s32", "s33", "s34", "s35", "s36", "s37", "s38", "s39", "s40", "s41", "s42", "s43", "s44", "s45", "s46", "s47", "s48", "s49", "s50", "s51", "s52", "s53", "s54", "s55", "s56", "s57", "s58", "s59", "s60", "s61", "s62", "s63", "s64", "s65", "s66", "s67", "s68", "s69", "s70", "s71", "s72", "s73", "s74", "s75", "s76", "s77", "s78", "s79", "s80", "s81", "s82", "s83", "s84", "s85", "s86", "s87", "s88", "s89", "s90", "s91", "s92", "s93", "s94", "s95", "s96", "s97", "s98", "s99", "s100")), 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 | Tissue` = new("dgCMatrix", i = c(0L, 2L, 2L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 2L, 0L, 0L, 1L, 1L, 2L, 2L, 0L, 0L, 2L, 2L, 2L, 2L, 1L, 1L, 0L, 1L, 2L, 1L, 2L, 1L, 2L, 0L, 1L, 1L, 2L, 2L, 0L, 0L, 0L, 1L, 1L, 0L, 2L, 1L, 1L, 0L, 0L, 2L, 1L, 0L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 0L, 1L, 2L, 1L, 1L, 0L, 1L, 2L, 1L, 0L, 1L, 2L, 2L, 0L, 0L, 1L, 2L, 2L, 0L, 2L, 2L, 2L, 0L, 1L, 0L), p = 0:100, Dim = c(3L, 100L), Dimnames = list(c("A", "B", "C"), c("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20", "s21", "s22", "s23", "s24", "s25", "s26", "s27", "s28", "s29", "s30", "s31", "s32", "s33", "s34", "s35", "s36", "s37", "s38", "s39", "s40", "s41", "s42", "s43", "s44", "s45", "s46", "s47", "s48", "s49", "s50", "s51", "s52", "s53", "s54", "s55", "s56", "s57", "s58", "s59", "s60", "s61", "s62", "s63", "s64", "s65", "s66", "s67", "s68", "s69", "s70", "s71", "s72", "s73", "s74", "s75", "s76", "s77", "s78", "s79", "s80", "s81", "s82", "s83", "s84", "s85", "s86", "s87", "s88", "s89", "s90", "s91", "s92", "s93", "s94", "s95", "s96", "s97", "s98", "s99", "s100")), 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(Individual = 25L, Tissue = 3L)), REML = FALSE, wmsgs = character(0), start = NULL, verbose = 0L, control = list(optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = FALSE, 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 = "stop.deficient", 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 = "ignore", 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(form.local, data, weights = w.local, control = control, na.action = na.action, REML = REML)
12: run_lmm_on_gene(it.init(), form, data, control = control, na.action = stats::na.exclude, REML = REML, fxn = identity, dreamCheck = dreamCheck)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch({ run_lmm_on_gene(it.init(), form, data, control = control, na.action = stats::na.exclude, REML = REML, fxn = identity, dreamCheck = dreamCheck)}, warning = function(w) errMsg <<- w$message, error = function(e) errMsg <<- e$message)
20: run_lmm(objFlt$exprObj, objFlt$formula, objFlt$data, REML = REML, fxn = fxn, dreamCheck = TRUE, control = control, BPPARAM = BPPARAM, ...)
21: .fitVarPartModel(exprObj, formula, data, REML = REML, useWeights = useWeights, fxn = fxn, control = control, hideErrorsInBackend = hideErrorsInBackend, BPPARAM = BPPARAM, ...)
22: fitVarPartModel(geneExpr[1:2, ], form, info)
23: fitVarPartModel(geneExpr[1:2, ], form, info)
24: eval(expr, envir, enclos)
25: eval(expr, envir, enclos)
26: eval_with_user_handlers(expr, envir, enclos, user_handlers)
27: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
28: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
29: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
30: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
31: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
32: evaluate::evaluate(...)
33: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
34: in_dir(input_dir(), expr)
35: 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$render, options)))
36: eng_r(options)
37: block_exec(params)
38: call_block(x)
39: process_group.block(group)
40: process_group(group)
41: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
42: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
43: 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]))
44: process_file(text, output)
45: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
46: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
47: vweave_rmarkdown(...)
48: engine$weave(file, quiet = quiet, encoding = enc)
49: doTryCatch(return(expr), name, parentenv, handler)
50: tryCatchOne(expr, names, parentenv, handlers[[1L]])
51: tryCatchList(expr, classes, parentenv, handlers)
52: tryCatch({ engine$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)))})
53: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
