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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ANCOMBC
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* checking for file ‘ANCOMBC/DESCRIPTION’ ... OK
* preparing ‘ANCOMBC’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: ANCOMBC
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘ANCOM.Rmd’ using rmarkdown
Quitting from lines 221-232 [unnamed-chunk-5] (ANCOM.Rmd)
Error: processing vignette 'ANCOM.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘ANCOM.Rmd’
--- re-building ‘ANCOMBC.Rmd’ using rmarkdown
Warning in sd : closing unused connection 6 (<-localhost:11551)
Warning in sd : closing unused connection 5 (<-localhost:11551)
--- finished re-building ‘ANCOMBC.Rmd’
--- re-building ‘ANCOMBC2.Rmd’ using rmarkdown
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0)
2: initializePtr()
3: .Object$initialize(...)
4: initialize(value, ...)
5: initialize(value, ...)
6: methods::new(def, ...)
7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(4L, 5L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 6L, 7L, 10L, 11L, 18L, 19L, 6L, 7L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 8L, 9L, 12L, 13L, 8L, 9L, 14L, 15L, 14L, 15L, 16L, 17L, 66L, 67L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 6L, 7L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 2L, 3L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 2L, 3L, 10L, 11L, 18L, 19L, 68L, 69L, 70L, 71L, 72L, 73L, 18L, 19L, 68L, 69L, 74L, 75L, 6L, 7L, 74L, 75L, 66L, 67L, 74L, 75L, 2L, 3L, 6L, 7L, 10L, 11L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 8L, 9L, 14L, 15L, 14L, 15L, 14L, 15L, 14L, 15L, 4L, 5L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 20L, 21L, 24L, 25L, 28L, 29L, 34L, 35L, 44L, 45L, 32L, 33L, 34L, 35L, 44L, 45L, 32L, 33L, 34L, 35L, 44L, 45L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L), 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, 202L, 204L, 206L, 208L, 210L, 212L, 214L, 216L, 218L, 220L, 222L, 224L, 226L, 228L, 230L, 232L, 234L, 236L, 238L, 240L, 242L, 244L, 246L, 248L, 250L, 252L, 254L, 256L, 258L, 260L, 262L, 264L, 266L, 268L, 270L, 272L, 274L, 276L, 278L, 280L, 282L, 284L, 286L, 288L, 290L, 292L, 294L, 296L, 298L, 300L, 302L, 304L, 306L, 308L, 310L, 312L, 314L, 316L, 318L, 320L, 322L, 324L, 326L, 328L, 330L, 332L, 334L, 336L, 338L, 340L, 342L, 344L, 346L, 348L, 350L, 352L, 354L, 356L, 358L, 360L, 362L, 364L, 366L, 368L, 370L, 372L, 374L, 376L, 378L, 380L, 382L, 384L, 386L, 388L, 390L, 392L, 394L, 396L, 398L, 400L, 402L, 404L, 406L, 408L, 410L, 412L, 414L, 416L, 418L, 420L, 422L, 424L, 426L, 428L, 430L, 432L, 434L, 436L, 438L, 440L, 442L, 444L), Dim = c(76L, 222L), Dimnames = list( c("azh", "azh", "azl", "azl", "byn", "byn", "byu", "byu", "cxj", "cxj", "dwc", "dwc", "dwk", "dwk", "eve", "eve", "fua", "fua", "fud", "fud", "gtd", "gtd", "gty", "gty", "hsf", "hsf", "irh", "irh", "irq", "irq", "jql", "jql", "jqr", "jqr", "kpb", "kpb", "kpp", "kpp", "lot", "lot", "lox", "lox", "mni", "mni", "mnk", "mnk", "nms", "nms", "nmz", "nmz", "olg", "olg", "olt", "olt", "pku", "pku", "qjy", "qjy", "riv", "riv", "shj", "shj", "tgx", "tgx", "ufm", "ufm", "vem", "vem", "wdf", "wdf", "xcw", "xcw", "ybg", "ybg", "zaq", "zaq"), c("Sample-1", "Sample-2", "Sample-3", "Sample-4", "Sample-5", "Sample-6", "Sample-7", "Sample-8", "Sample-9", "Sample-10", "Sample-11", "Sample-12", "Sample-13", "Sample-14", "Sample-15", "Sample-16", "Sample-17", "Sample-18", "Sample-19", "Sample-20", "Sample-21", "Sample-22", "Sample-23", "Sample-24", "Sample-25", "Sample-26", "Sample-27", "Sample-28", "Sample-29", "Sample-30", "Sample-31", "Sample-32", "Sample-33", "Sample-34", "Sample-35", "Sample-36", "Sample-37", "Sample-38", "Sample-39", "Sample-40", "Sample-41", "Sample-42", "Sample-43", "Sample-44", "Sample-45", "Sample-46", "Sample-47", "Sample-48", "Sample-49", "Sample-50", "Sample-51", "Sample-52", "Sample-53", "Sample-54", "Sample-55", "Sample-56", "Sample-57", "Sample-58", "Sample-59", "Sample-60", "Sample-61", "Sample-62", "Sample-63", "Sample-64", "Sample-65", "Sample-66", "Sample-67", "Sample-68", "Sample-69", "Sample-70", "Sample-71", "Sample-72", "Sample-73", "Sample-74", "Sample-75", "Sample-76", "Sample-77", "Sample-78", "Sample-79", "Sample-80", "Sample-81", "Sample-82", "Sample-83", "Sample-84", "Sample-85", "Sample-86", "Sample-87", "Sample-88", "Sample-89", "Sample-90", "Sample-91", "Sample-92", "Sample-93", "Sample-94", "Sample-95", "Sample-96", "Sample-97", "Sample-98", "Sample-99", "Sample-100", "Sample-101", "Sample-102", "Sample-103", "Sample-104", "Sample-105", "Sample-106", "Sample-107", "Sample-108", "Sample-109", "Sample-110", "Sample-111", "Sample-112", "Sample-113", "Sample-114", "Sample-115", "Sample-116", "Sample-117", "Sample-118", "Sample-119", "Sample-120", "Sample-121", "Sample-122", "Sample-123", "Sample-124", "Sample-125", "Sample-126", "Sample-127", "Sample-128", "Sample-129", "Sample-130", "Sample-131", "Sample-132", "Sample-133", "Sample-134", "Sample-135", "Sample-136", "Sample-137", "Sample-138", "Sample-139", "Sample-140", "Sample-141", "Sample-142", "Sample-143", "Sample-144", "Sample-145", "Sample-146", "Sample-147", "Sample-148", "Sample-149", "Sample-150", "Sample-151", "Sample-152", "Sample-153", "Sample-154", "Sample-155", "Sample-156", "Sample-157", "Sample-158", "Sample-159", "Sample-160", "Sample-161", "Sample-162", "Sample-163", "Sample-164", "Sample-165", "Sample-166", "Sample-167", "Sample-168", "Sample-169", "Sample-170", "Sample-171", "Sample-172", "Sample-173", "Sample-174", "Sample-175", "Sample-176", "Sample-177", "Sample-178", "Sample-179", "Sample-180", "Sample-181", "Sample-182", "Sample-183", "Sample-184", "Sample-185", "Sample-186", "Sample-187", "Sample-188", "Sample-189", "Sample-190", "Sample-191", "Sample-192", "Sample-193", "Sample-194", "Sample-195", "Sample-196", "Sample-197", "Sample-198", "Sample-199", "Sample-200", "Sample-201", "Sample-202", "Sample-203", "Sample-204", "Sample-205", "Sample-206", "Sample-207", "Sample-208", "Sample-209", "Sample-210", "Sample-211", "Sample-212", "Sample-213", "Sample-214", "Sample-215", "Sample-216", "Sample-217", "Sample-218", "Sample-219", "Sample-220", "Sample-221", "Sample-222" )), x = c(1, 4, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 6, 1, 1, 1, 6, 1, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 5, 1, 5, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 2, 1, 3, 1, 4, 1, 5, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 5, 1, 5, 1, 5, 1, 5, 1, 4, 1, 4, 1, 4, 1, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 6, 1, 6, 1, 6, 1, 2, 1, 2, 1, 3, 1, 3, 1, 4, 1, 4, 1, 5, 1, 5, 1, 1, 1, 1, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6), factors = list()), theta = c(1, 0, 1), Lambdat = new("dgCMatrix", i = c(0L, 0L, 1L, 2L, 2L, 3L, 4L, 4L, 5L, 6L, 6L, 7L, 8L, 8L, 9L, 10L, 10L, 11L, 12L, 12L, 13L, 14L, 14L, 15L, 16L, 16L, 17L, 18L, 18L, 19L, 20L, 20L, 21L, 22L, 22L, 23L, 24L, 24L, 25L, 26L, 26L, 27L, 28L, 28L, 29L, 30L, 30L, 31L, 32L, 32L, 33L, 34L, 34L, 35L, 36L, 36L, 37L, 38L, 38L, 39L, 40L, 40L, 41L, 42L, 42L, 43L, 44L, 44L, 45L, 46L, 46L, 47L, 48L, 48L, 49L, 50L, 50L, 51L, 52L, 52L, 53L, 54L, 54L, 55L, 56L, 56L, 57L, 58L, 58L, 59L, 60L, 60L, 61L, 62L, 62L, 63L, 64L, 64L, 65L, 66L, 66L, 67L, 68L, 68L, 69L, 70L, 70L, 71L, 72L, 72L, 73L, 74L, 74L, 75L), p = c(0L, 1L, 3L, 4L, 6L, 7L, 9L, 10L, 12L, 13L, 15L, 16L, 18L, 19L, 21L, 22L, 24L, 25L, 27L, 28L, 30L, 31L, 33L, 34L, 36L, 37L, 39L, 40L, 42L, 43L, 45L, 46L, 48L, 49L, 51L, 52L, 54L, 55L, 57L, 58L, 60L, 61L, 63L, 64L, 66L, 67L, 69L, 70L, 72L, 73L, 75L, 76L, 78L, 79L, 81L, 82L, 84L, 85L, 87L, 88L, 90L, 91L, 93L, 94L, 96L, 97L, 99L, 100L, 102L, 103L, 105L, 106L, 108L, 109L, 111L, 112L, 114L), Dim = c(76L, 76L), Dimnames = list(NULL, NULL), x = c(1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1), factors = list()), Lind = c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L), n = 222L, 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, 0, 1, 1, 1, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 6, 1, 6, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 5, 5, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 4, 5, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 4, 4, 4, 4, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 4, 5, 5, 5, 6, 6, 6, 2, 2, 3, 3, 4, 4, 5, 5, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
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_crt = c(-0.881976165519867, 0.802363055087351, 0.432344695974934, 1.77282952106353, -0.727825485692609, -0.999759201176251, -0.51425138539455, -0.371150541753877, -0.827908944249592, 1.05596581388627, -0.553472098547831, -0.188828984959922, -0.405052093429558, 2.41591619966656, -1.82643777436072, -0.881976165519867, 0.0777996782940265, 1.75708116409539, -0.338360718930886, -0.371150541753877, -0.881976165519867, 0.963850524978464, -0.134761763689646, 1.25153259743024, 0.011841710502229, 1.50576673581448, -0.188828984959922, -1.46976283042199, -1.82643777436072, 0.749440653633008, -1.46976283042199, 1.525969443132, 2.21661349347383, -0.24598739879987, 2.8792239501737, -1.13329059380077, -0.058775856711724, -0.999759201176251, -0.058775856711724, 2.11929628840974, 2.89588032500137, -1.28744127362803, 0.81261955525454, -0.24598739879987, -0.338360718930886, 0.321996638806068, -0.0111478077224696, 0.216636123148243, 0.862381064813604, -1.57512334607981, -1.37445265061766, 0.011841710502229, 0.447159781760075, 0.545140190120278, -0.405052093429558, -2.67373563474792, -0.161430010771808, 0.0988530874918592, -1.37445265061766, -0.0111478077224696, -1.57512334607981, -1.82643777436072, -0.553472098547831, -0.371150541753877, 0.011841710502229, 0.159477709308294, -0.216999861926618, -0.0111478077224696, -0.476511057411703, 0.981242267690333, -1.06429772231382, 0.704988891062175, -0.594294093068086, -1.37445265061766, 1.67006978710576, -0.636853707486882, -0.058775856711724, -0.594294093068086, -0.134761763689646, -0.275840361949552, -0.371150541753877, -1.46976283042199, 1.2112586982923, 2.18865741620724, 0.338525940757279, 0.760251569737224, -1.06429772231382, -0.594294093068086, -1.98058845418798, 0.159477709308294, 0.402039346479605, -0.338360718930886, -1.06429772231382, -2.38605356229614, -1.82643777436072, 0.178895795165396, 0.760251569737224, 0.19794399013609, -1.28744127362803, 3.1090633802265, -0.827908944249592, 0.011841710502229, -1.37445265061766, -2.67373563474792, 0.234985261816439, 0.0343145663542876, -1.28744127362803, -0.681305470057716, 0.178895795165396, 1.16212600971466, 0.0777996782940265, 0.338525940757279, -0.727825485692609, 0.781528968184509, -0.134761763689646, 0.0777996782940265, -0.636853707486882, -0.371150541753877, 3.20119509610411, 0.402039346479605, 3.03999717076145, -0.776615649862041, -0.0834684693020957, 0.58436090327356, 1.80738190257019, 2.39516856747231, 0.571457498437652, -0.553472098547831, 1.42060892747418, 4.05409521203998, 2.46010009313449, 0.305189520489688, -0.161430010771808, 0.531717169788138, -1.37445265061766, 0.842772593425228, 1.56519015628529, -0.727825485692609, -0.134761763689646, 4.10124986626951, 2.26313350910872, 0.0988530874918592, 0.634371323848221, 2.59926392381582, -0.827908944249592, -0.51425138539455, 1.27750808383351, 0.646492684380566, 2.19635963656933, -0.999759201176251, 0.270703344418518, 0.0777996782940265, 0.928132442376385, 0.0343145663542876, -0.216999861926618, 1.32751850440817, 0.0562934730730631, 0.727461746914233, -1.98058845418798, 0.0777996782940265, 0.963850524978464, -0.440143413240828, 0.011841710502229, -0.776615649862041, 0.178895795165396, -0.881976165519867, 3.32932804820341, -2.16291001098193, 1.3867073757985, -0.476511057411703, 0.852624889868239, -0.594294093068086, 1.11045399917034, -0.161430010771808, 0.461758581181228, -0.776615649862041, 1.2965562788042, -0.405052093429558, -0.134761763689646, -0.24598739879987, -0.939134579359816, -0.275840361949552, 1.2112586982923, 0.402039346479605, 0.760251569737224, -1.37445265061766, -1.57512334607981, -0.881976165519867, -0.371150541753877, -1.06429772231382, -0.827908944249592, -1.13329059380077, -0.188828984959922, -0.594294093068086, -0.134761763689646, -1.37445265061766, -0.216999861926618, -1.82643777436072, 0.270703344418518, -1.98058845418798, 1.43165876366076, -1.2073985659545, 0.402039346479605, -2.38605356229614, 0.432344695974934, -1.98058845418798, -0.727825485692609, -0.999759201176251, -1.13329059380077, -0.553472098547831, 0.321996638806068, 0.011841710502229, -0.108786277286386, -0.939134579359816, 1.46939909164361, 0.38653515994364, -0.338360718930886, -1.28744127362803, -1.06429772231382, -0.681305470057716, 0.545140190120278, 0.0343145663542876), nationality = c(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, 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, 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, 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, 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), timepoint = c(4L, 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, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 1L, 1L, 1L, 6L, 6L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 6L, 6L, 6L, 6L, 6L, 1L, 1L, 6L, 1L, 6L, 1L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 5L, 5L, 2L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 2L, 3L, 4L, 5L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 6L, 6L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 1L, 1L, 6L, 6L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L), group = c(1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), subject = c(3L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 4L, 6L, 10L, 4L, 6L, 10L, 34L, 35L, 36L, 37L, 38L, 2L, 34L, 35L, 36L, 37L, 38L, 2L, 5L, 7L, 5L, 8L, 8L, 9L, 34L, 36L, 37L, 38L, 2L, 4L, 6L, 10L, 34L, 35L, 36L, 37L, 2L, 6L, 10L, 34L, 35L, 36L, 37L, 2L, 6L, 10L, 35L, 36L, 37L, 10L, 35L, 38L, 4L, 38L, 34L, 38L, 2L, 4L, 6L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 5L, 7L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 5L, 7L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 5L, 7L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 5L, 8L, 8L, 8L, 8L, 3L, 9L, 11L, 13L, 15L, 17L, 18L, 23L, 9L, 11L, 13L, 15L, 17L, 18L, 23L, 9L, 11L, 13L, 15L, 9L, 11L, 13L, 15L, 9L, 11L, 13L, 15L, 17L, 18L, 23L, 11L, 13L, 15L, 18L, 23L, 17L, 18L, 23L, 17L, 18L, 23L, 14L, 16L, 14L, 16L, 14L, 16L, 14L, 16L, 14L, 16L, 14L, 16L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L)), 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, 0, 1, 1, 1, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 6, 1, 6, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 5, 5, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 4, 5, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 4, 4, 4, 4, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 4, 5, 5, 5, 6, 6, 6, 2, 2, 3, 3, 4, 4, 5, 5, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), reTrms = list(Zt = new("dgCMatrix", i = c(4L, 5L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 6L, 7L, 10L, 11L, 18L, 19L, 6L, 7L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 8L, 9L, 12L, 13L, 8L, 9L, 14L, 15L, 14L, 15L, 16L, 17L, 66L, 67L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 6L, 7L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 2L, 3L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 2L, 3L, 10L, 11L, 18L, 19L, 68L, 69L, 70L, 71L, 72L, 73L, 18L, 19L, 68L, 69L, 74L, 75L, 6L, 7L, 74L, 75L, 66L, 67L, 74L, 75L, 2L, 3L, 6L, 7L, 10L, 11L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 8L, 9L, 14L, 15L, 14L, 15L, 14L, 15L, 14L, 15L, 4L, 5L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 20L, 21L, 24L, 25L, 28L, 29L, 34L, 35L, 44L, 45L, 32L, 33L, 34L, 35L, 44L, 45L, 32L, 33L, 34L, 35L, 44L, 45L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L), 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, 202L, 204L, 206L, 208L, 210L, 212L, 214L, 216L, 218L, 220L, 222L, 224L, 226L, 228L, 230L, 232L, 234L, 236L, 238L, 240L, 242L, 244L, 246L, 248L, 250L, 252L, 254L, 256L, 258L, 260L, 262L, 264L, 266L, 268L, 270L, 272L, 274L, 276L, 278L, 280L, 282L, 284L, 286L, 288L, 290L, 292L, 294L, 296L, 298L, 300L, 302L, 304L, 306L, 308L, 310L, 312L, 314L, 316L, 318L, 320L, 322L, 324L, 326L, 328L, 330L, 332L, 334L, 336L, 338L, 340L, 342L, 344L, 346L, 348L, 350L, 352L, 354L, 356L, 358L, 360L, 362L, 364L, 366L, 368L, 370L, 372L, 374L, 376L, 378L, 380L, 382L, 384L, 386L, 388L, 390L, 392L, 394L, 396L, 398L, 400L, 402L, 404L, 406L, 408L, 410L, 412L, 414L, 416L, 418L, 420L, 422L, 424L, 426L, 428L, 430L, 432L, 434L, 436L, 438L, 440L, 442L, 444L), Dim = c(76L, 222L), Dimnames = list(c("azh", "azh", "azl", "azl", "byn", "byn", "byu", "byu", "cxj", "cxj", "dwc", "dwc", "dwk", "dwk", "eve", "eve", "fua", "fua", "fud", "fud", "gtd", "gtd", "gty", "gty", "hsf", "hsf", "irh", "irh", "irq", "irq", "jql", "jql", "jqr", "jqr", "kpb", "kpb", "kpp", "kpp", "lot", "lot", "lox", "lox", "mni", "mni", "mnk", "mnk", "nms", "nms", "nmz", "nmz", "olg", "olg", "olt", "olt", "pku", "pku", "qjy", "qjy", "riv", "riv", "shj", "shj", "tgx", "tgx", "ufm", "ufm", "vem", "vem", "wdf", "wdf", "xcw", "xcw", "ybg", "ybg", "zaq", "zaq"), c("Sample-1", "Sample-2", "Sample-3", "Sample-4", "Sample-5", "Sample-6", "Sample-7", "Sample-8", "Sample-9", "Sample-10", "Sample-11", "Sample-12", "Sample-13", "Sample-14", "Sample-15", "Sample-16", "Sample-17", "Sample-18", "Sample-19", "Sample-20", "Sample-21", "Sample-22", "Sample-23", "Sample-24", "Sample-25", "Sample-26", "Sample-27", "Sample-28", "Sample-29", "Sample-30", "Sample-31", "Sample-32", "Sample-33", "Sample-34", "Sample-35", "Sample-36", "Sample-37", "Sample-38", "Sample-39", "Sample-40", "Sample-41", "Sample-42", "Sample-43", "Sample-44", "Sample-45", "Sample-46", "Sample-47", "Sample-48", "Sample-49", "Sample-50", "Sample-51", "Sample-52", "Sample-53", "Sample-54", "Sample-55", "Sample-56", "Sample-57", "Sample-58", "Sample-59", "Sample-60", "Sample-61", "Sample-62", "Sample-63", "Sample-64", "Sample-65", "Sample-66", "Sample-67", "Sample-68", "Sample-69", "Sample-70", "Sample-71", "Sample-72", "Sample-73", "Sample-74", "Sample-75", "Sample-76", "Sample-77", "Sample-78", "Sample-79", "Sample-80", "Sample-81", "Sample-82", "Sample-83", "Sample-84", "Sample-85", "Sample-86", "Sample-87", "Sample-88", "Sample-89", "Sample-90", "Sample-91", "Sample-92", "Sample-93", "Sample-94", "Sample-95", "Sample-96", "Sample-97", "Sample-98", "Sample-99", "Sample-100", "Sample-101", "Sample-102", "Sample-103", "Sample-104", "Sample-105", "Sample-106", "Sample-107", "Sample-108", "Sample-109", "Sample-110", "Sample-111", "Sample-112", "Sample-113", "Sample-114", "Sample-115", "Sample-116", "Sample-117", "Sample-118", "Sample-119", "Sample-120", "Sample-121", "Sample-122", "Sample-123", "Sample-124", "Sample-125", "Sample-126", "Sample-127", "Sample-128", "Sample-129", "Sample-130", "Sample-131", "Sample-132", "Sample-133", "Sample-134", "Sample-135", "Sample-136", "Sample-137", "Sample-138", "Sample-139", "Sample-140", "Sample-141", "Sample-142", "Sample-143", "Sample-144", "Sample-145", "Sample-146", "Sample-147", "Sample-148", "Sample-149", "Sample-150", "Sample-151", "Sample-152", "Sample-153", "Sample-154", "Sample-155", "Sample-156", "Sample-157", "Sample-158", "Sample-159", "Sample-160", "Sample-161", "Sample-162", "Sample-163", "Sample-164", "Sample-165", "Sample-166", "Sample-167", "Sample-168", "Sample-169", "Sample-170", "Sample-171", "Sample-172", "Sample-173", "Sample-174", "Sample-175", "Sample-176", "Sample-177", "Sample-178", "Sample-179", "Sample-180", "Sample-181", "Sample-182", "Sample-183", "Sample-184", "Sample-185", "Sample-186", "Sample-187", "Sample-188", "Sample-189", "Sample-190", "Sample-191", "Sample-192", "Sample-193", "Sample-194", "Sample-195", "Sample-196", "Sample-197", "Sample-198", "Sample-199", "Sample-200", "Sample-201", "Sample-202", "Sample-203", "Sample-204", "Sample-205", "Sample-206", "Sample-207", "Sample-208", "Sample-209", "Sample-210", "Sample-211", "Sample-212", "Sample-213", "Sample-214", "Sample-215", "Sample-216", "Sample-217", "Sample-218", "Sample-219", "Sample-220", "Sample-221", "Sample-222")), x = c(1, 4, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 6, 1, 1, 1, 6, 1, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 5, 1, 5, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 2, 1, 3, 1, 4, 1, 5, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 5, 1, 5, 1, 5, 1, 5, 1, 4, 1, 4, 1, 4, 1, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 6, 1, 6, 1, 6, 1, 2, 1, 2, 1, 3, 1, 3, 1, 4, 1, 4, 1, 5, 1, 5, 1, 1, 1, 1, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6), factors = list()), theta = c(1, 0, 1), Lind = c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L), Gp = c(0L, 76L), lower = c(0, -Inf, 0), Lambdat = new("dgCMatrix", i = c(0L, 0L, 1L, 2L, 2L, 3L, 4L, 4L, 5L, 6L, 6L, 7L, 8L, 8L, 9L, 10L, 10L, 11L, 12L, 12L, 13L, 14L, 14L, 15L, 16L, 16L, 17L, 18L, 18L, 19L, 20L, 20L, 21L, 22L, 22L, 23L, 24L, 24L, 25L, 26L, 26L, 27L, 28L, 28L, 29L, 30L, 30L, 31L, 32L, 32L, 33L, 34L, 34L, 35L, 36L, 36L, 37L, 38L, 38L, 39L, 40L, 40L, 41L, 42L, 42L, 43L, 44L, 44L, 45L, 46L, 46L, 47L, 48L, 48L, 49L, 50L, 50L, 51L, 52L, 52L, 53L, 54L, 54L, 55L, 56L, 56L, 57L, 58L, 58L, 59L, 60L, 60L, 61L, 62L, 62L, 63L, 64L, 64L, 65L, 66L, 66L, 67L, 68L, 68L, 69L, 70L, 70L, 71L, 72L, 72L, 73L, 74L, 74L, 75L), p = c(0L, 1L, 3L, 4L, 6L, 7L, 9L, 10L, 12L, 13L, 15L, 16L, 18L, 19L, 21L, 22L, 24L, 25L, 27L, 28L, 30L, 31L, 33L, 34L, 36L, 37L, 39L, 40L, 42L, 43L, 45L, 46L, 48L, 49L, 51L, 52L, 54L, 55L, 57L, 58L, 60L, 61L, 63L, 64L, 66L, 67L, 69L, 70L, 72L, 73L, 75L, 76L, 78L, 79L, 81L, 82L, 84L, 85L, 87L, 88L, 90L, 91L, 93L, 94L, 96L, 97L, 99L, 100L, 102L, 103L, 105L, 106L, 108L, 109L, 111L, 112L, 114L ), Dim = c(76L, 76L), Dimnames = list(NULL, NULL), x = c(1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1), factors = list()), flist = list(subject = c(3L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 4L, 6L, 10L, 4L, 6L, 10L, 34L, 35L, 36L, 37L, 38L, 2L, 34L, 35L, 36L, 37L, 38L, 2L, 5L, 7L, 5L, 8L, 8L, 9L, 34L, 36L, 37L, 38L, 2L, 4L, 6L, 10L, 34L, 35L, 36L, 37L, 2L, 6L, 10L, 34L, 35L, 36L, 37L, 2L, 6L, 10L, 35L, 36L, 37L, 10L, 35L, 38L, 4L, 38L, 34L, 38L, 2L, 4L, 6L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 5L, 7L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 5L, 7L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 5L, 7L, 1L, 21L, 12L, 19L, 20L, 22L, 25L, 26L, 3L, 5L, 8L, 8L, 8L, 8L, 3L, 9L, 11L, 13L, 15L, 17L, 18L, 23L, 9L, 11L, 13L, 15L, 17L, 18L, 23L, 9L, 11L, 13L, 15L, 9L, 11L, 13L, 15L, 9L, 11L, 13L, 15L, 17L, 18L, 23L, 11L, 13L, 15L, 18L, 23L, 17L, 18L, 23L, 17L, 18L, 23L, 14L, 16L, 14L, 16L, 14L, 16L, 14L, 16L, 14L, 16L, 14L, 16L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 24L, 27L, 28L, 29L, 30L, 31L, 32L, 33L)), cnms = list(subject = c("(Intercept)", "timepoint")), Ztlist = list(`timepoint | subject` = new("dgCMatrix", i = c(4L, 5L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 6L, 7L, 10L, 11L, 18L, 19L, 6L, 7L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 8L, 9L, 12L, 13L, 8L, 9L, 14L, 15L, 14L, 15L, 16L, 17L, 66L, 67L, 70L, 71L, 72L, 73L, 74L, 75L, 2L, 3L, 6L, 7L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 2L, 3L, 10L, 11L, 18L, 19L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 2L, 3L, 10L, 11L, 18L, 19L, 68L, 69L, 70L, 71L, 72L, 73L, 18L, 19L, 68L, 69L, 74L, 75L, 6L, 7L, 74L, 75L, 66L, 67L, 74L, 75L, 2L, 3L, 6L, 7L, 10L, 11L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 8L, 9L, 12L, 13L, 0L, 1L, 40L, 41L, 22L, 23L, 36L, 37L, 38L, 39L, 42L, 43L, 48L, 49L, 50L, 51L, 4L, 5L, 8L, 9L, 14L, 15L, 14L, 15L, 14L, 15L, 14L, 15L, 4L, 5L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 16L, 17L, 20L, 21L, 24L, 25L, 28L, 29L, 32L, 33L, 34L, 35L, 44L, 45L, 20L, 21L, 24L, 25L, 28L, 29L, 34L, 35L, 44L, 45L, 32L, 33L, 34L, 35L, 44L, 45L, 32L, 33L, 34L, 35L, 44L, 45L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 26L, 27L, 30L, 31L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 46L, 47L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L), 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, 202L, 204L, 206L, 208L, 210L, 212L, 214L, 216L, 218L, 220L, 222L, 224L, 226L, 228L, 230L, 232L, 234L, 236L, 238L, 240L, 242L, 244L, 246L, 248L, 250L, 252L, 254L, 256L, 258L, 260L, 262L, 264L, 266L, 268L, 270L, 272L, 274L, 276L, 278L, 280L, 282L, 284L, 286L, 288L, 290L, 292L, 294L, 296L, 298L, 300L, 302L, 304L, 306L, 308L, 310L, 312L, 314L, 316L, 318L, 320L, 322L, 324L, 326L, 328L, 330L, 332L, 334L, 336L, 338L, 340L, 342L, 344L, 346L, 348L, 350L, 352L, 354L, 356L, 358L, 360L, 362L, 364L, 366L, 368L, 370L, 372L, 374L, 376L, 378L, 380L, 382L, 384L, 386L, 388L, 390L, 392L, 394L, 396L, 398L, 400L, 402L, 404L, 406L, 408L, 410L, 412L, 414L, 416L, 418L, 420L, 422L, 424L, 426L, 428L, 430L, 432L, 434L, 436L, 438L, 440L, 442L, 444L), Dim = c(76L, 222L), Dimnames = list( c("azh", "azh", "azl", "azl", "byn", "byn", "byu", "byu", "cxj", "cxj", "dwc", "dwc", "dwk", "dwk", "eve", "eve", "fua", "fua", "fud", "fud", "gtd", "gtd", "gty", "gty", "hsf", "hsf", "irh", "irh", "irq", "irq", "jql", "jql", "jqr", "jqr", "kpb", "kpb", "kpp", "kpp", "lot", "lot", "lox", "lox", "mni", "mni", "mnk", "mnk", "nms", "nms", "nmz", "nmz", "olg", "olg", "olt", "olt", "pku", "pku", "qjy", "qjy", "riv", "riv", "shj", "shj", "tgx", "tgx", "ufm", "ufm", "vem", "vem", "wdf", "wdf", "xcw", "xcw", "ybg", "ybg", "zaq", "zaq"), c("Sample-1", "Sample-2", "Sample-3", "Sample-4", "Sample-5", "Sample-6", "Sample-7", "Sample-8", "Sample-9", "Sample-10", "Sample-11", "Sample-12", "Sample-13", "Sample-14", "Sample-15", "Sample-16", "Sample-17", "Sample-18", "Sample-19", "Sample-20", "Sample-21", "Sample-22", "Sample-23", "Sample-24", "Sample-25", "Sample-26", "Sample-27", "Sample-28", "Sample-29", "Sample-30", "Sample-31", "Sample-32", "Sample-33", "Sample-34", "Sample-35", "Sample-36", "Sample-37", "Sample-38", "Sample-39", "Sample-40", "Sample-41", "Sample-42", "Sample-43", "Sample-44", "Sample-45", "Sample-46", "Sample-47", "Sample-48", "Sample-49", "Sample-50", "Sample-51", "Sample-52", "Sample-53", "Sample-54", "Sample-55", "Sample-56", "Sample-57", "Sample-58", "Sample-59", "Sample-60", "Sample-61", "Sample-62", "Sample-63", "Sample-64", "Sample-65", "Sample-66", "Sample-67", "Sample-68", "Sample-69", "Sample-70", "Sample-71", "Sample-72", "Sample-73", "Sample-74", "Sample-75", "Sample-76", "Sample-77", "Sample-78", "Sample-79", "Sample-80", "Sample-81", "Sample-82", "Sample-83", "Sample-84", "Sample-85", "Sample-86", "Sample-87", "Sample-88", "Sample-89", "Sample-90", "Sample-91", "Sample-92", "Sample-93", "Sample-94", "Sample-95", "Sample-96", "Sample-97", "Sample-98", "Sample-99", "Sample-100", "Sample-101", "Sample-102", "Sample-103", "Sample-104", "Sample-105", "Sample-106", "Sample-107", "Sample-108", "Sample-109", "Sample-110", "Sample-111", "Sample-112", "Sample-113", "Sample-114", "Sample-115", "Sample-116", "Sample-117", "Sample-118", "Sample-119", "Sample-120", "Sample-121", "Sample-122", "Sample-123", "Sample-124", "Sample-125", "Sample-126", "Sample-127", "Sample-128", "Sample-129", "Sample-130", "Sample-131", "Sample-132", "Sample-133", "Sample-134", "Sample-135", "Sample-136", "Sample-137", "Sample-138", "Sample-139", "Sample-140", "Sample-141", "Sample-142", "Sample-143", "Sample-144", "Sample-145", "Sample-146", "Sample-147", "Sample-148", "Sample-149", "Sample-150", "Sample-151", "Sample-152", "Sample-153", "Sample-154", "Sample-155", "Sample-156", "Sample-157", "Sample-158", "Sample-159", "Sample-160", "Sample-161", "Sample-162", "Sample-163", "Sample-164", "Sample-165", "Sample-166", "Sample-167", "Sample-168", "Sample-169", "Sample-170", "Sample-171", "Sample-172", "Sample-173", "Sample-174", "Sample-175", "Sample-176", "Sample-177", "Sample-178", "Sample-179", "Sample-180", "Sample-181", "Sample-182", "Sample-183", "Sample-184", "Sample-185", "Sample-186", "Sample-187", "Sample-188", "Sample-189", "Sample-190", "Sample-191", "Sample-192", "Sample-193", "Sample-194", "Sample-195", "Sample-196", "Sample-197", "Sample-198", "Sample-199", "Sample-200", "Sample-201", "Sample-202", "Sample-203", "Sample-204", "Sample-205", "Sample-206", "Sample-207", "Sample-208", "Sample-209", "Sample-210", "Sample-211", "Sample-212", "Sample-213", "Sample-214", "Sample-215", "Sample-216", "Sample-217", "Sample-218", "Sample-219", "Sample-220", "Sample-221", "Sample-222" )), x = c(1, 4, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 1, 1, 1, 1, 6, 1, 1, 1, 6, 1, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 5, 1, 5, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 1, 2, 1, 3, 1, 4, 1, 5, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 3, 1, 5, 1, 5, 1, 5, 1, 5, 1, 4, 1, 4, 1, 4, 1, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 4, 1, 4, 1, 5, 1, 5, 1, 5, 1, 6, 1, 6, 1, 6, 1, 2, 1, 2, 1, 3, 1, 3, 1, 4, 1, 4, 1, 5, 1, 5, 1, 1, 1, 1, 1, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6), factors = list())), nl = c(subject = 38L)), 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 = tformula, data = data.frame(y_crt = y[1, ], meta_data), control = lme_control)
12: eval(expr, p)
13: eval(expr, p)
14: eval.parent(mc)
15: lmerTest::lmer(formula = tformula, data = data.frame(y_crt = y[1, ], meta_data), control = lme_control)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch({ result <- lmerTest::lmer(formula = tformula, data = data.frame(y_crt = y[1, ], meta_data), control = lme_control)}, error = function(e) { message <- sprintf(paste("Encountering the error for `lmerTest` package.", "Please try to select one of your taxa and use its raw counts to fix the same linear mixed-effects model using `lmerTest` without the `ANCOMBC` package.", "Load all necessary packages EXCEPT `ANCOMBC`, and see if the error arises due to package incompatibility or other issues.", "The error message from `lmerTest` is as follows:", e$message, sep = "\n")) stop(message, call. = FALSE)})
20: .iter_remle(x = x, y = y1, meta_data = meta_data, fix_formula = fix_formula, rand_formula = rand_formula, lme_control = lme_control, theta = NULL, tol = iter_control$tol, max_iter = iter_control$max_iter, verbose = iter_control$verbose)
21: ancombc2(data = tse, assay_name = "counts", tax_level = "Family", fix_formula = "nationality + timepoint + group", rand_formula = "(timepoint | subject)", p_adj_method = "holm", pseudo_sens = TRUE, prv_cut = 0.1, lib_cut = 1000, s0_perc = 0.05, group = "group", struc_zero = TRUE, neg_lb = TRUE, alpha = 0.05, n_cl = 2, verbose = TRUE, global = TRUE, pairwise = TRUE, dunnet = TRUE, trend = TRUE, iter_control = list(tol = 0.01, max_iter = 20, verbose = TRUE), em_control = list(tol = 1e-05, max_iter = 100), lme_control = lme4::lmerControl(), mdfdr_control = list(fwer_ctrl_method = "holm", B = 100), trend_control = list(contrast = list(matrix(c(1, 0, -1, 1), nrow = 2, byrow = TRUE)), node = list(2), solver = "ECOS", B = 10))
22: eval(expr, envir, enclos)
23: eval(expr, envir, enclos)
24: eval_with_user_handlers(expr, envir, enclos, user_handlers)
25: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
26: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
27: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
28: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
29: evaluate_call(expr, parsed$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)
30: evaluate::evaluate(...)
31: 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$render, options))
32: in_dir(input_dir(), expr)
33: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
34: eng_r(options)
35: block_exec(params)
36: call_block(x)
37: process_group.block(group)
38: process_group(group)
39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
40: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))})
41: handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]))
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: 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)))})
51: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
