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This page was generated on 2024-03-28 11:40:06 -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
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Package 2026/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.27.1  (landing page)
Luke Zappia
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/splatter
git_branch: devel
git_last_commit: ea842a2
git_last_commit_date: 2024-03-26 16:18:58 -0400 (Tue, 26 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for splatter on lconway


To the developers/maintainers of the splatter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/splatter.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.

raw results


Summary

Package: splatter
Version: 1.27.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings splatter_1.27.1.tar.gz
StartedAt: 2024-03-28 00:18:44 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 00:25:11 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 387.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: splatter.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings splatter_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/splatter.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 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     36.287  0.627  37.185
BASiCSSimulate    6.056  0.280   6.395
mockBulkeQTL      5.749  0.535   6.347
kersplatEstimate  5.165  0.193   5.390
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 47794 Segmentation fault: 11  ${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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/splatter.Rcheck/00check.log’
for details.


Installation output

splatter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL splatter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

splatter.Rcheck/tests/spelling.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  0.234   0.090   0.310 

splatter.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 0x0, cause 'unknown'

Traceback:
 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind,     RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta,     u0)
 2: initializePtr()
 3: .Object$initialize(...)
 4: initialize(value, ...)
 5: initialize(value, ...)
 6: methods::new(def, ...)
 7: (new("refMethodDef", .Data = function (...) {    methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot",     superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 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(0.099415038869768, -0.379828545048838, 0.0565696897829142, -0.258408386822744, -0.0877856880672727, -0.061543992625483, 0.046118508036817, 0.124271161877116, 0.185563023618431, 0.0863593950919948, -0.56345492759145, -0.189566668681887, 0.345767454613878, -0.0372016838241394, -0.831886866637659, -0.0440024012845792, 0.0613439280644819, 0.165855683642866, 0.507531750908371, -1.63388034585584, -0.0386339210428579, -0.178769808549106, -0.0425102686041306, -0.351441593254914, 0.14095725379126, -0.26034419645512, 0.00166255613855808, -0.415477390512743, 0.346928632583233, -0.0864072091674503, -0.315932159081673, -0.362353549353006, -1.03144216141072, -0.0133032735950596, -0.268983625968043, -0.298709345622086, -0.231983628441647, 0.0454259104208528, -0.0967765348845144, 0.187307121445735, 0.320792525358586, 0.264803079837192, 0.0844968886935661, 0.0831660920106556, 0.164077650428171, -0.183924667792603, -0.014594381370487, 0.675728251106668, -0.013946110473825, -0.431604456155111, 0.383035094710592, -0.017585303406751, 0.177330480039961, -0.406149859243613, -0.602820074084561, -0.363704526604013, -0.354627231387144, -0.778615690929021, -0.0249333214810372, 0.125879376223266, -0.146611868232665, 0.494738747027579, 0.264539745647939, -0.0138339579865562, -0.0604923897108628, 0.531143769641901, -0.593642871849057, -0.262127296526215, -0.300470213862321, -0.658375555914743, 0.174298844139928, 0.114146943666202, -0.0124292692295182, -0.281796727453792, 0.0500745786980265, 0.487278679759632, -0.414002615442896, 0.123918150393643, -1.67445131941827, -0.379312963276262, 0.338238089202279, -0.0280385241180911, 0.491652947938528, 0.166221014704874, 0.0684744686639439, -0.499231203535198, 0.544133310959025, 0.191440739948786, -0.207407409381184, 0.229531947788602, -0.0744338695765945, 0.26291083158208, -0.176558738508868, -0.0165011025009814, -0.241101747569872, -0.374537883964343, 0.217453927920594, 0.0916019299158345, -0.267169816259059, 0.28168700573108, 0.083552451542729, 0.177536610172399, 0.147078865094902, 0.18084870055571, 0.215486382213473, -0.0670453434445629, 0.0706094552105798, -0.169274626291377, -0.292817173334925, -0.0152435039760019, -0.24875605596651, -0.0460293642921873, -0.0553245236163159, 0.338374893785228, -0.27367726719201, -0.290627469059366, -0.20419510573265, 0.218431077035407, -0.31200368462525, -0.648966507946428, -0.313398141379113, -0.830242165624212, 0.225923023725423, 0.183029838140348, -0.447277964821486, -0.173375782776695, 0.00471047922889148, -0.321521187389957, 0.18196253465792, -0.0216396893215089, -0.351905863041009, -0.0192115633603184, 0.165829955476795, -0.173942913084997, -0.195331196655357, 0.176171914543302, -0.0795758985096257, 0.33155884934634, 0.19574447381189, 0.197774296858661, 0.0676302223084067, 0.407952554798438, 0.216850807866717, 0.00604410710748176, 0.803126522955307, 0.675728251106668, -0.372698050367551, 0.338630033620027, -0.216075753117768, 0.176081664524125, -0.253469961953984, -0.102201224725323, 0.0169984361044372, -0.0704423920086104, -0.0724707300008174, -0.121603175804744, -0.459532898869912, 0.139916591758436, -0.275667166793369, 0.1107731799318, -0.757129363510934, 0.0176135938565981, 0.1559824399534, 0.0636812033678214, -0.272654800281362, -0.156896086646592, -0.656250949898347, -0.145374157295841, 0.0926137350986882, 0.110450101702026, 0.391711886004828, -0.0611105358770773, -0.0499677364991217, -0.532172793155276, 0.058888807355348, 0.641706754959037, -0.238810405414909, -0.429164702074668, -0.468971467453558, 0.455665563044504, 0.234161398733825, 0.587380893468882, 0.394329769151368, -0.221856048734092, 0.129582289777065, -0.0867136784063051, 0.402820389425792, 0.160213846167719, -0.175785045410078, 0.0436768400925117, -0.407844509600082, 0.0988681398910556, -0.297252034675955, -0.0552115503889233, -0.00403808176848588, 0.278589302086595, -0.3961197682938, 0.157839055803157, -0.368190692687059, -0.169832650269634)), 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$tagwise[i]))        output <- unlist(lme4::VarCorr(out))        return(output)    }, error = function(err) {        output <- NA_real_        return(output)    })}, ARGS = list(), OPTIONS = list(log = FALSE, threshold = "INFO",     stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_,     force.GC = FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, -1607547610L, -1990829135L, 1269865556L, 1148056496L, -1774022817L, -420649453L), GLOBALS = list(), PACKAGES = character(0))
27: do.call(msg$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 ...

Example timings

splatter.Rcheck/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate000
BASiCSSimulate6.0560.2806.395
addGeneLengths0.4060.0170.426
compareSCEs2.7760.0912.885
diffSCEs3.0180.0383.079
getParam0.0000.0000.001
getParams000
kersplatEstimate5.1650.1935.390
kersplatSample1.8400.1362.000
kersplatSetup0.1560.0210.180
kersplatSimulate0.0010.0000.000
listSims0.0290.0040.034
lun2Estimate000
lun2Simulate0.4220.0470.478
lunEstimate0.5320.0230.562
lunSimulate0.3620.0120.378
makeCompPanel0.0010.0000.000
makeDiffPanel000
makeOverallPanel000
mfaEstimate0.1170.0150.133
mfaSimulate1.2270.1041.340
minimiseSCE1.6560.0671.738
mockBulkMatrix000
mockBulkeQTL5.7490.5356.347
mockEmpiricalSet3.4840.2623.781
mockGFF0.0030.0000.003
mockVCF0.1280.0010.129
newParams0.0020.0000.003
phenoEstimate0.6480.0180.672
phenoSimulate0.9300.0360.974
scDDEstimate36.287 0.62737.185
scDDSimulate0.0000.0010.000
setParam0.0110.0010.013
setParams0.0280.0020.030
simpleEstimate0.5580.0070.568
simpleSimulate0.5860.0100.598
sparseDCEstimate0.9750.0751.059
sparseDCSimulate1.9430.1252.082
splatEstimate3.3150.0943.433
splatPopEstimate3.2300.0963.349
splatPopQuantNorm0.0240.0010.026
splatPopSimulate000
splatPopSimulateMeans000
splatPopSimulateSC000
splatSimulate0.8330.0700.909
summariseDiff3.0620.0603.149
zinbEstimate2.3670.1082.490
zinbSimulate0.2190.0030.223