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This page was generated on 2024-03-28 11:40:28 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 412/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMethDMR 1.7.0  (landing page)
Fernanda Veitzman
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/coMethDMR
git_branch: devel
git_last_commit: b5ea1bb
git_last_commit_date: 2023-10-24 11:38:47 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  ERROR    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for coMethDMR on kunpeng2


To the developers/maintainers of the coMethDMR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coMethDMR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: coMethDMR
Version: 1.7.0
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data coMethDMR
StartedAt: 2024-03-27 21:43:20 -0000 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 21:47:09 -0000 (Wed, 27 Mar 2024)
EllapsedTime: 228.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data coMethDMR
###
##############################################################################
##############################################################################


* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* preparing ‘coMethDMR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x40ff4000000000c4, cause 'memory not mapped'

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, 0L, 22L, 0L, 24L, 1L, 20L, 21L, 1L, 22L, 23L, 1L, 24L, 25L, 2L, 20L, 21L, 2L, 22L, 23L, 2L, 24L, 25L, 3L, 20L, 21L, 3L, 22L, 23L, 3L, 24L, 25L, 4L, 20L, 21L, 4L, 22L, 23L, 4L, 24L, 25L, 5L, 20L, 21L, 5L, 22L, 23L, 5L, 24L, 25L, 6L, 20L, 21L, 6L, 22L, 23L, 6L, 24L, 25L, 7L, 20L, 21L, 7L, 22L, 23L, 7L, 24L, 25L, 8L, 20L, 21L, 8L, 22L, 23L, 8L, 24L, 25L, 9L, 20L, 9L, 22L, 9L, 24L, 10L, 20L, 21L, 10L, 22L, 23L, 10L, 24L, 25L, 11L, 20L, 21L, 11L, 22L, 23L, 11L, 24L, 25L, 12L, 20L, 21L, 12L, 22L, 23L, 12L, 24L, 25L, 13L, 20L, 21L, 13L, 22L, 23L, 13L, 24L, 25L, 14L, 20L, 21L, 14L, 22L, 23L, 14L, 24L, 25L, 15L, 20L, 21L, 15L, 22L, 23L, 15L, 24L, 25L, 16L, 20L, 21L, 16L, 22L, 23L, 16L, 24L, 25L, 17L, 20L, 21L, 17L, 22L, 23L, 17L, 24L, 25L, 18L, 20L, 21L, 18L, 22L, 23L, 18L, 24L, 25L, 19L, 20L, 21L, 19L, 22L, 23L, 19L, 24L, 25L), p = c(0L, 2L, 4L, 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, 80L, 82L, 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), Dim = c(26L, 60L), Dimnames = list(c("GSM1443251", "GSM1443279", "GSM1443326", "GSM1443332", "GSM1443364", "GSM1443387", "GSM1443389", "GSM1443434", "GSM1443455", "GSM1443475", "GSM1443485", "GSM1443503", "GSM1443547", "GSM1443573", "GSM1443577", "GSM1443640", "GSM1443643", "GSM1443663", "GSM1443683", "GSM1443685", "cg12460175", "cg12460175", "cg14086922", "cg14086922", "cg21463605", "cg21463605"), 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")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 3, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 3, 1, 1, 3, 1, 1, 3, 1, 1, 4, 1, 1, 4, 1, 1, 4, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 4, 1, 1, 4, 1, 1, 4, 1, 1, 3, 1, 1, 3, 1, 1, 3, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 2, 1, 1, 2, 1, 1, 2), factors = list()),     theta = c(1, 1, 0, 1), Lambdat = 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, 20L, 21L, 22L, 22L, 23L, 24L,     24L, 25L), p = c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L,     10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L,     23L, 24L, 26L, 27L, 29L), Dim = c(26L, 26L), 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, 0, 1, 1, 0, 1, 1, 0, 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, 3L, 4L, 2L, 3L, 4L, 2L,     3L, 4L), n = 60L, 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, 0, 0, 0, 3, 3, 3, 6, 6,     6, 6, 6, 6, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1,     0, 0, 0, 5, 5, 5, 3, 3, 3, 4, 4, 4, 6, 6, 6, 4, 4, 4, 3,     3, 3, 6, 6, 6, 5, 5, 5, 6, 6, 6, 2, 2, 2))
 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(Mvalue = c(1.52385444781284, 0.916011746882516, 1.1647056126548, 1.70263127360444, 1.01465707558817, 0.894539125852992, 1.79848485000947, 1.34575163456315, 1.18083883355375, 1.72957947453349, 1.07788987874182, 0.917968416357074, 1.98236551913908, 1.11699503818393, 1.29845711033221, 1.51713491166167, 0.992820674034694, 0.887152155647564, 2.12270751813623, 0.789809804284409, 0.991433226423634, 1.47537530331702, 0.418137402077866, 0.846912808715548, 1.76464955497061, 1.21000921022359, 1.38545920811999, 2.39614874628268, 1.92021751376038, 2.13130468100799, 1.34539495138156, 0.68655993398263, 0.356555663961402, 1.85686445384943, 1.53474987360238, 1.32353308628381, 1.77796288863869, 0.966703874899997, 0.785496471955168, 1.31043890598612, 0.791597267481503, 0.673246733030581, 1.59252367025177, 0.910984229436374, 0.770208042249653, 2.04830381394024, 1.69983696854856, 1.50917261808942, 2.30884595154281, 1.24312947453405, 1.4112565592468, 2.29707750241068, 1.51082205945175, 1.58572357464332, 1.31459319393046, 0.90679002760624, 0.751573331570821, 1.78254188601678, 0.949272970491747, 1.02871142627945), Sample = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 11L, 11L, 11L, 12L, 12L, 12L, 13L, 13L, 13L, 14L, 14L, 14L, 15L, 15L, 15L, 16L, 16L, 16L, 17L, 17L, 17L, 18L, 18L, 18L, 19L, 19L, 19L, 20L, 20L, 20L), stage = c(0, 0, 0, 3, 3, 3, 6, 6, 6, 6, 6, 6, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 0, 0, 0, 5, 5, 5, 3, 3, 3, 4, 4, 4, 6, 6, 6, 4, 4, 4, 3, 3, 3, 6, 6, 6, 5, 5, 5, 6, 6, 6, 2, 2, 2), ProbeID = 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)), 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, 0, 0, 0, 3, 3, 3, 6, 6, 6, 6, 6, 6, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 0, 0, 0, 5, 5, 5, 3, 3, 3, 4, 4, 4, 6, 6, 6, 4, 4, 4, 3, 3, 3, 6, 6, 6, 5, 5, 5, 6, 6, 6, 2, 2, 2), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 20L, 0L, 22L, 0L, 24L, 1L, 20L, 21L, 1L, 22L, 23L, 1L, 24L, 25L, 2L, 20L, 21L, 2L, 22L, 23L, 2L, 24L, 25L, 3L, 20L, 21L, 3L, 22L, 23L, 3L, 24L, 25L, 4L, 20L, 21L, 4L, 22L, 23L, 4L, 24L, 25L, 5L, 20L, 21L, 5L, 22L, 23L, 5L, 24L, 25L, 6L, 20L, 21L, 6L, 22L, 23L, 6L, 24L, 25L, 7L, 20L, 21L, 7L, 22L, 23L, 7L, 24L, 25L, 8L, 20L, 21L, 8L, 22L, 23L, 8L, 24L, 25L, 9L, 20L, 9L, 22L, 9L, 24L, 10L, 20L, 21L, 10L, 22L, 23L, 10L, 24L, 25L, 11L, 20L, 21L, 11L, 22L, 23L, 11L, 24L, 25L, 12L, 20L, 21L, 12L, 22L, 23L, 12L, 24L, 25L, 13L, 20L, 21L, 13L, 22L, 23L, 13L, 24L, 25L, 14L, 20L, 21L, 14L, 22L, 23L, 14L, 24L, 25L, 15L, 20L, 21L, 15L, 22L, 23L, 15L, 24L, 25L, 16L, 20L, 21L, 16L, 22L, 23L, 16L, 24L, 25L, 17L, 20L, 21L, 17L, 22L, 23L, 17L, 24L, 25L, 18L, 20L, 21L, 18L, 22L, 23L, 18L, 24L, 25L, 19L, 20L, 21L, 19L, 22L, 23L, 19L, 24L, 25L), p = c(0L, 2L, 4L, 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, 80L, 82L, 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), Dim = c(26L, 60L), Dimnames = list(c("GSM1443251", "GSM1443279", "GSM1443326", "GSM1443332", "GSM1443364", "GSM1443387", "GSM1443389", "GSM1443434", "GSM1443455", "GSM1443475", "GSM1443485", "GSM1443503", "GSM1443547", "GSM1443573", "GSM1443577", "GSM1443640", "GSM1443643", "GSM1443663", "GSM1443683", "GSM1443685", "cg12460175", "cg12460175", "cg14086922", "cg14086922", "cg21463605", "cg21463605"), 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")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 3, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 3, 1, 1, 3, 1, 1, 3, 1, 1, 4, 1, 1, 4, 1, 1, 4, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 4, 1, 1, 4, 1, 1, 4, 1, 1, 3, 1, 1, 3, 1, 1, 3, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 6, 1, 1, 6, 1, 1, 6, 1, 1, 2, 1, 1, 2, 1, 1, 2), factors = list()),     theta = c(1, 1, 0, 1), Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 3L,     4L, 2L, 3L, 4L, 2L, 3L, 4L), Gp = c(0L, 20L, 26L), lower = c(0,     0, -Inf, 0), Lambdat = 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, 20L, 21L, 22L, 22L, 23L, 24L, 24L,     25L), p = c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,     11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 23L,     24L, 26L, 27L, 29L), Dim = c(26L, 26L), 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, 0, 1, 1, 0, 1, 1, 0, 1), factors = list()),     flist = list(Sample = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L,     4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L, 8L,     9L, 9L, 9L, 10L, 10L, 10L, 11L, 11L, 11L, 12L, 12L, 12L,     13L, 13L, 13L, 14L, 14L, 14L, 15L, 15L, 15L, 16L, 16L, 16L,     17L, 17L, 17L, 18L, 18L, 18L, 19L, 19L, 19L, 20L, 20L, 20L    ), ProbeID = 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)), cnms = list(Sample = "(Intercept)", ProbeID = c("(Intercept)",     "stage")), Ztlist = list(`1 | Sample` = new("dgCMatrix",         i = c(0L, 0L, 0L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L,         4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L,         8L, 9L, 9L, 9L, 10L, 10L, 10L, 11L, 11L, 11L, 12L, 12L,         12L, 13L, 13L, 13L, 14L, 14L, 14L, 15L, 15L, 15L, 16L,         16L, 16L, 17L, 17L, 17L, 18L, 18L, 18L, 19L, 19L, 19L        ), p = 0:60, Dim = c(20L, 60L), Dimnames = list(c("GSM1443251",         "GSM1443279", "GSM1443326", "GSM1443332", "GSM1443364",         "GSM1443387", "GSM1443389", "GSM1443434", "GSM1443455",         "GSM1443475", "GSM1443485", "GSM1443503", "GSM1443547",         "GSM1443573", "GSM1443577", "GSM1443640", "GSM1443643",         "GSM1443663", "GSM1443683", "GSM1443685"), 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")), 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), factors = list()),         `stage | ProbeID` = new("dgCMatrix", i = c(0L, 2L, 4L,         0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L,         2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L,         4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L,         0L, 1L, 2L, 3L, 4L, 5L, 0L, 2L, 4L, 0L, 1L, 2L, 3L, 4L,         5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L,         1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L,         3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L,         5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),             p = c(0L, 1L, 2L, 3L, 5L, 7L, 9L, 11L, 13L, 15L,             17L, 19L, 21L, 23L, 25L, 27L, 29L, 31L, 33L, 35L,             37L, 39L, 41L, 43L, 45L, 47L, 49L, 51L, 52L, 53L,             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), Dim = c(6L, 60L), Dimnames = list(c("cg12460175",             "cg12460175", "cg14086922", "cg14086922", "cg21463605",             "cg21463605"), 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")),             x = c(1, 1, 1, 1, 3, 1, 3, 1, 3, 1, 6, 1, 6, 1, 6,             1, 6, 1, 6, 1, 6, 1, 5, 1, 5, 1, 5, 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, 1, 1, 1, 5, 1, 5, 1, 5, 1, 3, 1, 3, 1, 3,             1, 4, 1, 4, 1, 4, 1, 6, 1, 6, 1, 6, 1, 4, 1, 4, 1,             4, 1, 3, 1, 3, 1, 3, 1, 6, 1, 6, 1, 6, 1, 5, 1, 5,             1, 5, 1, 6, 1, 6, 1, 6, 1, 2, 1, 2, 1, 2), factors = list())),     nl = c(Sample = 20L, ProbeID = 3L)), 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 = as.formula(modelFormula_char), data = betaOnePheno_df)
12: eval(expr, p)
13: eval(expr, p)
14: eval.parent(mc)
15: lmer(as.formula(modelFormula_char), betaOnePheno_df)
16: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
17: suppressMessages(lmer(as.formula(modelFormula_char), betaOnePheno_df))
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch({    suppressMessages(lmer(as.formula(modelFormula_char), betaOnePheno_df))}, error = function(e) {    NULL})
22: FUN(...)
23: withCallingHandlers({    ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)()    FUN(...)}, error = function(e) {    annotated_condition <- handle_error(e)    stop(annotated_condition)}, warning = handle_warning)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch({    withCallingHandlers({        ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)()        FUN(...)    }, error = function(e) {        annotated_condition <- handle_error(e)        stop(annotated_condition)    }, warning = handle_warning)}, error = identity)
28: FUN(X[[i]], ...)