##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings splatter_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/splatter.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘splatter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘splatter’ version ‘1.27.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘splatter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' calls not declared from:
  ‘GenomicFeatures’ ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
scDDEstimate     42.361  0.164  42.617
BASiCSSimulate    6.461  0.092   6.566
mockBulkeQTL      6.247  0.140   6.401
kersplatEstimate  5.972  0.119   6.103
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’/home/biocbuild/R/R-4.4-devel-2024.03.20/bin/BATCH: line 60: 2713801 Segmentation fault      (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  76: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  77: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  78: source_file(path, env = env(env), desc = desc, error_call = error_call)
  79: FUN(X[[i]], ...)
  80: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  81: doTryCatch(return(expr), name, parentenv, handler)
  82: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  83: tryCatchList(expr, classes, parentenv, handlers)
  84: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  85: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  86: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  87: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  88: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  89: test_check("splatter")
  An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/splatter.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL splatter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘splatter’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (splatter)

R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE, error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.237   0.006   0.227 

R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(splatter)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("splatter")

 *** 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, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L), p = 0:200, Dim = c(2L, 200L), Dimnames = list(    c("1", "2"), c("1", "2", "3", "4", "5", "6", "7", "8", "9",     "10", "11", "12", "13", "14", "15", "16", "17", "18", "19",     "20", "21", "22", "23", "24", "25", "26", "27", "28", "29",     "30", "31", "32", "33", "34", "35", "36", "37", "38", "39",     "40", "41", "42", "43", "44", "45", "46", "47", "48", "49",     "50", "51", "52", "53", "54", "55", "56", "57", "58", "59",     "60", "61", "62", "63", "64", "65", "66", "67", "68", "69",     "70", "71", "72", "73", "74", "75", "76", "77", "78", "79",     "80", "81", "82", "83", "84", "85", "86", "87", "88", "89",     "90", "91", "92", "93", "94", "95", "96", "97", "98", "99",     "100", "101", "102", "103", "104", "105", "106", "107", "108",     "109", "110", "111", "112", "113", "114", "115", "116", "117",     "118", "119", "120", "121", "122", "123", "124", "125", "126",     "127", "128", "129", "130", "131", "132", "133", "134", "135",     "136", "137", "138", "139", "140", "141", "142", "143", "144",     "145", "146", "147", "148", "149", "150", "151", "152", "153",     "154", "155", "156", "157", "158", "159", "160", "161", "162",     "163", "164", "165", "166", "167", "168", "169", "170", "171",     "172", "173", "174", "175", "176", "177", "178", "179", "180",     "181", "182", "183", "184", "185", "186", "187", "188", "189",     "190", "191", "192", "193", "194", "195", "196", "197", "198",     "199", "200")), 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 = 1, Lambdat = new("dgCMatrix",     i = 0:1, p = 0:2, Dim = c(2L, 2L), Dimnames = list(NULL,         NULL), x = c(1, 1), factors = list()), Lind = c(1L, 1L), n = 200L, X = numeric(0))
 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")],     n = nrow(X), list(X = X)))
 9: (function (fr, X, reTrms, family, nAGQ = 1L, verbose = 0L, maxit = 100L,     control = glmerControl(), ...) {    stopifnot(length(nAGQ <- as.integer(nAGQ)) == 1L, 0L <= nAGQ,         nAGQ <= 25L)    verbose <- as.integer(verbose)    maxit <- as.integer(maxit)    rho <- list2env(list(verbose = verbose, maxit = maxit, tolPwrss = control$tolPwrss,         compDev = control$compDev), parent = parent.frame())    rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta",         "Lambdat", "Lind")], n = nrow(X), list(X = X)))    rho$resp <- if (missing(fr))         mkRespMod(family = family, ...)    else mkRespMod(fr, family = family)    nAGQinit <- if (control$nAGQ0initStep)         0L    else 1L    if (length(y <- rho$resp$y) > 0) {        checkResponse(y, control$checkControl)        rho$verbose <- as.integer(verbose)        .Call(glmerLaplace, rho$pp$ptr(), rho$resp$ptr(), nAGQinit,             control$tolPwrss, maxit, verbose)        rho$lp0 <- rho$pp$linPred(1)        rho$pwrssUpdate <- glmerPwrssUpdate    }    rho$lower <- reTrms$lower    mkdevfun(rho, nAGQinit, maxit = maxit, verbose = verbose,         control = control)})(fr = list(Counts = c(2L, 38L, 7L, 121L, 22L, 6L, 4L, 64L, 2L, 150L, 202L, 23L, 4L, 14L, 121L, 13L, 8L, 8L, 242L, 0L, 0L, 49L, 31L, 109L, 13L, 4L, 0L, 111L, 77L, 3L, 47L, 24L, 20L, 9L, 18L, 411L, 1L, 66L, 22L, 7L, 47L, 0L, 341L, 17L, 27L, 0L, 3L, 0L, 91L, 26L, 24L, 0L, 25L, 2L, 24L, 56L, 160L, 75L, 28L, 21L, 53L, 23L, 0L, 128L, 23L, 25L, 86L, 1L, 254L, 390L, 27L, 107L, 576L, 211L, 9L, 29L, 44L, 2L, 33L, 42L, 42L, 43L, 82L, 2L, 222L, 86L, 34L, 0L, 0L, 2L, 41L, 8L, 70L, 153L, 13L, 3L, 5L, 2L, 50L, 0L, 0L, 135L, 125L, 28L, 53L, 93L, 32L, 4L, 119L, 24L, 2L, 9L, 196L, 19L, 28L, 2L, 5L, 266L, 350L, 355L, 54L, 47L, 7L, 0L, 0L, 175L, 104L, 233L, 0L, 135L, 35L, 4L, 2L, 0L, 14L, 0L, 26L, 55L, 267L, 8L, 5L, 0L, 120L, 27L, 269L, 3L, 6L, 1L, 4L, 0L, 12L, 1L, 8L, 14L, 34L, 17L, 222L, 83L, 249L, 160L, 3L, 10L, 24L, 25L, 20L, 154L, 128L, 9L, 15L, 40L, 2L, 55L, 0L, 15L, 59L, 2L, 312L, 17L, 168L, 293L, 13L, 20L, 13L, 74L, 52L, 111L, 11L, 25L, 3L, 0L, 172L, 91L, 10L, 125L, 50L, 105L, 129L, 4L, 5L, 1L), Plate = c(1, 1, 1, 1, 1, 2, 1, 2, 1, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 2, 1, 2, 2, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 1, 1, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 2, 2, 1, 2, 1, 1, 2, 2, 2, 2, 1, 2, 1, 1, 2, 1, 1, 2, 1, 2, 2, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 2, 1, 1, 2, 1, 1, 2, 2, 2, 2, 1, 1, 2, 2, 2, 1, 2, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 2, 2, 2, 1, 2, 2, 2, 2), `offset(log(sum.facs))` = c(0.0994150389172455, -0.379828544988215, 0.0565696898347931, -0.258408386768051, -0.0877856879996709, -0.0615439926030457, 0.0461185080827268, 0.124271161914752, 0.185563023671502, 0.0863593951324114, -0.563454927535015, -0.189566668629049, 0.34576745466456, -0.0372016837703739, -0.831886866587634, -0.0440024012586887, 0.0613439281122787, 0.165855683690811, 0.507531750953593, -1.63388039218876, -0.0386339210082325, -0.178769808503883, -0.0425102685589188, -0.351441593146645, 0.140957253829817, -0.260344196406601, 0.00166255618656218, -0.415477390478957, 0.346928632630215, -0.0864072091191802, -0.315932159022762, -0.36235354932273, -1.03144216135881, -0.0133032735437494, -0.268983625938496, -0.298709345571795, -0.231983628395484, 0.0454259104507471, -0.0967765348068013, 0.187307121491481, 0.320792525409603, 0.264803079868387, 0.0844968887345989, 0.0831660920558701, 0.164077650483565, -0.183924667758987, -0.014594381318711, 0.675728251151887, -0.0139461104189381, -0.431604456125766, 0.383035094755814, -0.0175853033712759, 0.177330480086928, -0.40614985919735, -0.602820074039342, -0.363704526539228, -0.354627231370286, -0.778615690883795, -0.0249333214101483, 0.1258793762475, -0.146611868210474, 0.494738747095209, 0.264539745683073, -0.013833957949972, -0.0604923896741236, 0.531143769687121, -0.593642871799062, -0.262127296503069, -0.300470213832723, -0.658375555876551, 0.174298844187836, 0.114146943713796, -0.0124292691771715, -0.281796727408577, 0.0500745787911934, 0.48727867981099, -0.41400261538549, 0.123918150447365, -1.67445131937303, -0.379312963231036, 0.338238089243289, -0.028038524036436, 0.491652947983743, 0.166221014756159, 0.0684744687028144, -0.499231203511623, 0.544133311004247, 0.191440739994004, -0.207407409320897, 0.229531947826639, -0.0744338695241862, 0.262910831619085, -0.17655873845321, -0.0165011024606169, -0.241101747513735, -0.374537883935498, 0.217453927968249, 0.0916019299491485, -0.267169816186392, 0.281687005772422, 0.0835524515742906, 0.177536610242824, 0.147078865130887, 0.180848700609946, 0.215486382258687, -0.0670453433885662, 0.0706094552557973, -0.169274626238048, -0.292817173286475, -0.0152435039285684, -0.248756055889347, -0.0460293642469682, -0.0553245235434469, 0.338374893820984, -0.273677267146789, -0.290627469011053, -0.20419510570218, 0.218431077070658, -0.312003684592727, -0.648966507901208, -0.313398141330646, -0.830242165589572, 0.22592302378078, 0.183029838193474, -0.447277964810159, -0.173375782739991, 0.00471047926925689, -0.321521187359599, 0.18196253469352, -0.0216396892805492, -0.351905863018098, -0.0192115633196346, 0.165829955524815, -0.173942913046207, -0.195331196602321, 0.176171914589191, -0.0795758984395697, 0.331558849391555, 0.195744473857745, 0.197774296884401, 0.0676302223400344, 0.407952554836229, 0.216850807946397, 0.00604410717854068, 0.803126522995264, 0.675728251151887, -0.372698050265682, 0.338630033654205, -0.216075753088673, 0.176081664569344, -0.253469961919059, -0.102201224696243, 0.0169984361375506, -0.0704423919545038, -0.0724707299699951, -0.121603175769885, -0.459532898832909, 0.139916591838379, -0.2756671667674, 0.110773179963909, -0.757129363463441, 0.0176135939115411, 0.155982439980236, 0.0636812034005881, -0.272654800226356, -0.156896086616411, -0.656250949853126, -0.145374157270112, 0.0926137351279904, 0.110450101727778, 0.391711886051941, -0.0611105358500269, -0.0499677364511175, -0.532172793130821, 0.0588888074059719, 0.641706755004728, -0.238810405381965, -0.429164702028425, -0.468971467431977, 0.455665563079194, 0.234161398786051, 0.587380893514101, 0.394329769203751, -0.221856048674641, 0.12958228981405, -0.0867136783361771, 0.402820389450869, 0.16021384621862, -0.175785045351614, 0.0436768401225914, -0.407844509566212, 0.0988681399690017, -0.297252034640065, -0.0552115503428101, -0.00403808173657147, 0.278589302134051, -0.396119768248584, 0.157839055838964, -0.368190692640968, -0.169832650214695)),     X = numeric(0), reTrms = list(Zt = new("dgCMatrix", i = c(0L,     0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 1L,     0L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,     0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 1L,     1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L,     0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L,     0L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L,     1L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L,     1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 1L, 0L,     0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L,     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L,     1L, 1L, 1L, 1L), p = 0:200, Dim = c(2L, 200L), Dimnames = list(        c("1", "2"), c("1", "2", "3", "4", "5", "6", "7", "8",         "9", "10", "11", "12", "13", "14", "15", "16", "17",         "18", "19", "20", "21", "22", "23", "24", "25", "26",         "27", "28", "29", "30", "31", "32", "33", "34", "35",         "36", "37", "38", "39", "40", "41", "42", "43", "44",         "45", "46", "47", "48", "49", "50", "51", "52", "53",         "54", "55", "56", "57", "58", "59", "60", "61", "62",         "63", "64", "65", "66", "67", "68", "69", "70", "71",         "72", "73", "74", "75", "76", "77", "78", "79", "80",         "81", "82", "83", "84", "85", "86", "87", "88", "89",         "90", "91", "92", "93", "94", "95", "96", "97", "98",         "99", "100", "101", "102", "103", "104", "105", "106",         "107", "108", "109", "110", "111", "112", "113", "114",         "115", "116", "117", "118", "119", "120", "121", "122",         "123", "124", "125", "126", "127", "128", "129", "130",         "131", "132", "133", "134", "135", "136", "137", "138",         "139", "140", "141", "142", "143", "144", "145", "146",         "147", "148", "149", "150", "151", "152", "153", "154",         "155", "156", "157", "158", "159", "160", "161", "162",         "163", "164", "165", "166", "167", "168", "169", "170",         "171", "172", "173", "174", "175", "176", "177", "178",         "179", "180", "181", "182", "183", "184", "185", "186",         "187", "188", "189", "190", "191", "192", "193", "194",         "195", "196", "197", "198", "199", "200")), 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 = 1,         Lind = c(1L, 1L), Gp = c(0L, 2L), lower = 0, Lambdat = new("dgCMatrix",             i = 0:1, p = 0:2, Dim = c(2L, 2L), Dimnames = list(                NULL, NULL), x = c(1, 1), factors = list()),         flist = list(Plate = c(1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L,         1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L,         2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L,         2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L,         1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,         2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L,         2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,         1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L,         2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L,         1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L,         1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L,         1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L,         2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L,         1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L,         2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L)), cnms = list(            Plate = "(Intercept)"), Ztlist = list(`1 | Plate` = new("dgCMatrix",             i = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 1L,             0L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 0L, 1L, 1L,             1L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L,             1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 0L,             0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L,             1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L,             0L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L,             0L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 0L,             0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L,             0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L,             1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,             1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L,             0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L,             0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,             0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L,             1L, 1L, 0L, 1L, 1L, 1L, 1L), p = 0:200, Dim = c(2L,             200L), Dimnames = list(c("1", "2"), c("1", "2", "3",             "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",             "14", "15", "16", "17", "18", "19", "20", "21", "22",             "23", "24", "25", "26", "27", "28", "29", "30", "31",             "32", "33", "34", "35", "36", "37", "38", "39", "40",             "41", "42", "43", "44", "45", "46", "47", "48", "49",             "50", "51", "52", "53", "54", "55", "56", "57", "58",             "59", "60", "61", "62", "63", "64", "65", "66", "67",             "68", "69", "70", "71", "72", "73", "74", "75", "76",             "77", "78", "79", "80", "81", "82", "83", "84", "85",             "86", "87", "88", "89", "90", "91", "92", "93", "94",             "95", "96", "97", "98", "99", "100", "101", "102",             "103", "104", "105", "106", "107", "108", "109",             "110", "111", "112", "113", "114", "115", "116",             "117", "118", "119", "120", "121", "122", "123",             "124", "125", "126", "127", "128", "129", "130",             "131", "132", "133", "134", "135", "136", "137",             "138", "139", "140", "141", "142", "143", "144",             "145", "146", "147", "148", "149", "150", "151",             "152", "153", "154", "155", "156", "157", "158",             "159", "160", "161", "162", "163", "164", "165",             "166", "167", "168", "169", "170", "171", "172",             "173", "174", "175", "176", "177", "178", "179",             "180", "181", "182", "183", "184", "185", "186",             "187", "188", "189", "190", "191", "192", "193",             "194", "195", "196", "197", "198", "199", "200")),             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())),         nl = c(Plate = 2L)), family = list(family = "Negative Binomial(0.4099)",         link = "log", linkfun = function (mu)         log(mu), linkinv = function (eta)         pmax(exp(eta), .Machine$double.eps), variance = function (mu)         mu + mu^2/.Theta, dev.resids = function (y, mu, wt)         2 * wt * (y * log(pmax(1, y)/mu) - (y + .Theta) * log((y +             .Theta)/(mu + .Theta))), aic = function (y, n, mu,             wt, dev)         {            term <- (y + .Theta) * log(mu + .Theta) - y * log(mu) +                 lgamma(y + 1) - .Theta * log(.Theta) + lgamma(.Theta) -                 lgamma(.Theta + y)            2 * sum(term * wt)        }, mu.eta = function (eta)         pmax(exp(eta), .Machine$double.eps), initialize = expression(            {                if (any(y < 0))                   stop("negative values not allowed for the negative binomial family")                n <- rep(1, nobs)                mustart <- y + (y == 0)/6            }), validmu = function (mu)         all(mu > 0), valideta = function (eta)         TRUE, simulate = function (object, nsim)         {            ftd <- fitted(object)            rnegbin(nsim * length(ftd), ftd, .Theta)        }), wmsgs = character(0), verbose = 0L, control = list(        optimizer = c("bobyqa", "Nelder_Mead"), restart_edge = FALSE,         boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE,         checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop",             check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop",             check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols",             check.scaleX = "warning", check.formula.LHS = "stop",             check.response.not.const = "stop"), checkConv = list(            check.conv.grad = list(action = "warning", tol = 0.002,                 relTol = NULL), check.conv.singular = list(action = "message",                 tol = 1e-04), check.conv.hess = list(action = "warning",                 tol = 1e-06)), optCtrl = list(), tolPwrss = 1e-07,         compDev = TRUE, nAGQ0initStep = TRUE), nAGQ = 0L)
10: do.call(mkGlmerDevfun, c(glmod, list(verbose = verbose, control = control,     nAGQ = nAGQinit)))
11: lme4::glmer(Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),     data = data.frame(Counts = as.integer(counts[i, ]), Group = groups,         Plate = plates), family = lme4::negative.binomial(1/dge$tagwise[i]))
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch({    out <- lme4::glmer(Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),         data = data.frame(Counts = as.integer(counts[i, ]), Group = groups,             Plate = plates), family = lme4::negative.binomial(1/dge$tagwise[i]))    output <- unlist(lme4::VarCorr(out))    return(output)}, error = function(err) {    output <- NA_real_    return(output)})
16: FUN(...)
17: withCallingHandlers({    ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)()    FUN(...)}, error = function(e) {    annotated_condition <- handle_error(e)    stop(annotated_condition)}, warning = handle_warning)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: 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)
22: FUN(X[[i]], ...)
23: (function (X, FUN, ...) {    FUN <- match.fun(FUN)    if (!is.vector(X) || is.object(X))         X <- as.list(X)    .Internal(lapply(X, FUN))})(X = 1:100, FUN = function (...) {    if (!identical(timeout, WORKER_TIMEOUT)) {        setTimeLimit(timeout, timeout, TRUE)        on.exit(setTimeLimit(Inf, Inf, FALSE))    }    if (!is.null(globalOptions))         base::options(globalOptions)    if (stop.on.error && ERROR_OCCURRED) {        UNEVALUATED    }    else {        .rng_reset_generator("L'Ecuyer-CMRG", SEED)        output <- 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)        if (force.GC)             gc(verbose = FALSE, full = FALSE)        SEED <<- .rng_next_substream(SEED)        output    }})
24: do.call(lapply, args)
25: BiocParallel:::.workerLapply_impl(...)
26: (function (...) BiocParallel:::.workerLapply_impl(...))(X = 1:100, FUN = function (i) {    if (progress) {        pb$tick()    }    tryCatch({        out <- lme4::glmer(Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),             data = data.frame(Counts = as.integer(counts[i, ]),                 Group = groups, Plate = plates), family = lme4::negative.binomial(1/dge$tagwise[i]))        output <- unlist(lme4::VarCorr(out))        return(output)    }, error = function(err) {        output <- NA_real_        return(output)    })}, ARGS = list(), OPTIONS = list(log = FALSE, threshold = "INFO",     stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_,     force.GC = FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, -977952920L, -1769025828L, 2051817236L, 1876552795L, 2145456353L, 2063973599L), GLOBALS = list(), PACKAGES = character(0))
27: do.call(msg$data$fun, msg$data$args)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch({    do.call(msg$data$fun, msg$data$args)}, error = function(e) {    list(.error_worker_comm(e, "worker evaluation failed"))})
32: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
33: .recv_any(manager$backend)
34: .recv_any(manager$backend)
35: .manager_recv(manager)
36: .manager_recv(manager)
37: .collect_result(manager, reducer, progress, BPPARAM)
38: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,     BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer,     progress.length = length(redo_index))
39: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS,     ...)
40: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
41: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,     BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
42: bplapply(seq_len(nrow(dge)), function(i) {    if (progress) {        pb$tick()    }    tryCatch({        out <- lme4::glmer(Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),             data = data.frame(Counts = as.integer(counts[i, ]),                 Group = groups, Plate = plates), family = lme4::negative.binomial(1/dge$tagwise[i]))        output <- unlist(lme4::VarCorr(out))        return(output)    }, error = function(err) {        output <- NA_real_        return(output)    })}, BPPARAM = BPPARAM)
43: bplapply(seq_len(nrow(dge)), function(i) {    if (progress) {        pb$tick()    }    tryCatch({        out <- lme4::glmer(Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),             data = data.frame(Counts = as.integer(counts[i, ]),                 Group = groups, Plate = plates), family = lme4::negative.binomial(1/dge$tagwise[i]))        output <- unlist(lme4::VarCorr(out))        return(output)    }, error = function(err) {        output <- NA_real_        return(output)    })}, BPPARAM = BPPARAM)
44: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
45: suppressWarnings(collected <- bplapply(seq_len(nrow(dge)), function(i) {    if (progress) {        pb$tick()    }    tryCatch({        out <- lme4::glmer(Counts ~ 0 + (1 | Plate) + offset(log(sum.facs)),             data = data.frame(Counts = as.integer(counts[i, ]),                 Group = groups, Plate = plates), family = lme4::negative.binomial(1/dge$tagwise[i]))        output <- unlist(lme4::VarCorr(out))        return(output)    }, error = function(err) {        output <- NA_real_        return(output)    })}, BPPARAM = BPPARAM))
46: lun2Estimate.matrix(counts, plates, params, min.size = min.size,     verbose = verbose, BPPARAM = BPPARAM)
47: lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose,     BPPARAM = BPPARAM)
48: lun2Estimate.SingleCellExperiment(sce, plates, min.size = 20)
49: lun2Estimate(sce, plates, min.size = 20)
50: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
51: withCallingHandlers(code, warning = function(condition) {    if (ignore_deprecation && is_deprecation(condition)) {        return()    }    out$push(condition)    maybe_restart("muffleWarning")})
52: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),     ...)
53: quasi_capture(enquo(object), label, capture_warnings, ignore_deprecation = identical(regexp,     NA))
54: expect_warning(lun2Estimate(sce, plates, min.size = 20), "more singular values")
55: eval(code, test_env)
56: eval(code, test_env)
57: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
58: doTryCatch(return(expr), name, parentenv, handler)
59: tryCatchOne(expr, names, parentenv, handlers[[1L]])
60: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
61: doTryCatch(return(expr), name, parentenv, handler)
62: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
63: tryCatchList(expr, classes, parentenv, handlers)
64: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
65: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
66: test_that("lun2Estimate works", {    plates <- as.numeric(factor(colData(sce)$Mutation_Status))    params <- expect_warning(lun2Estimate(sce, plates, min.size = 20),         "more singular values")    expect_true(validObject(params))})
67: eval(code, test_env)
68: eval(code, test_env)
69: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
70: doTryCatch(return(expr), name, parentenv, handler)
71: tryCatchOne(expr, names, parentenv, handlers[[1L]])
72: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
73: doTryCatch(return(expr), name, parentenv, handler)
74: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
75: tryCatchList(expr, classes, parentenv, handlers)
76: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
77: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
78: source_file(path, env = env(env), desc = desc, error_call = error_call)
79: FUN(X[[i]], ...)
80: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
81: doTryCatch(return(expr), name, parentenv, handler)
82: tryCatchOne(expr, names, parentenv, handlers[[1L]])
83: tryCatchList(expr, classes, parentenv, handlers)
84: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
85: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
86: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
87: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
88: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
89: test_check("splatter")
An irrecoverable exception occurred. R is aborting now ...