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This page was generated on 2024-03-27 11:36:56 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 1148/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.29.0  (landing page)
Andrew McDavid
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/MAST
git_branch: devel
git_last_commit: 0c17e9a
git_last_commit_date: 2023-10-24 10:53:20 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for MAST on nebbiolo1


To the developers/maintainers of the MAST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAST.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: MAST
Version: 1.29.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MAST_1.29.0.tar.gz
StartedAt: 2024-03-26 23:51:16 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 23:59:38 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 502.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MAST.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MAST_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MAST.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ version ‘1.29.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAST’ 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 ... WARNING
Missing or unexported object: ‘gdata::xls2csv’
* 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 ... NOTE
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
       |                                        ^
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
       |                                                                ^
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
       |                                                                                                                        ^
* 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  30: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  31: source_file(path, env = env(env), desc = desc, error_call = error_call)
  32: FUN(X[[i]], ...)
  33: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  34: doTryCatch(return(expr), name, parentenv, handler)
  35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  36: tryCatchList(expr, classes, parentenv, handlers)
  37: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  38: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  39: 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)
  40: 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)
  41: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  42: test_check("MAST")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/MAST.Rcheck/00check.log’
for details.


Installation output

MAST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MAST
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘MAST’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (MAST)

Tests output

MAST.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-pc-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.

> library(testthat)
> test_check("MAST")
Loading required package: MAST
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


 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind,     RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta,     u0)
 2: initializePtr()
 3: .Object$initialize(...)
 4: initialize(value, ...)
 5: initialize(value, ...)
 6: methods::new(def, ...)
 7: (new("refMethodDef", .Data = function (...) {    methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot",     superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), p = 0:175,     Dim = c(2L, 175L), Dimnames = list(c("Sub01", "Sub02"), c("Sub01 1 Stim(SEB) CD154+VbetaResponsive A10 1",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive B02 1", "Sub01 1 Stim(SEB) CD154+VbetaResponsive B06 1",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive B08 1", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H05 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H06 100", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H07 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H08 100", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H09 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H10 100", "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive G11 100",     "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive G12 100", "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive H01 100",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive B09 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive B11 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive B12 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C01 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C03 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C05 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C07 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C09 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C10 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive D01 1",     "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H02 100", "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H03 100",     "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H04 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive A01 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive A02 1", "Sub01 2 Stim(SEB) CD154+VbetaResponsive A08 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive A12 1", "Sub01 2 Stim(SEB) CD154+VbetaResponsive B07 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H05 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H06 100",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H07 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H08 100",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H09 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H10 100",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D06 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D09 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D11 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E01 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E02 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E05 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E06 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E07 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E10 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E11 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive G11 100", "Sub01 2 Stim(SEB) CD154-VbetaResponsive B12 1",     "Sub01 2 Stim(SEB) CD154-VbetaResponsive C05 1", "Sub01 2 Stim(SEB) CD154-VbetaResponsive C09 1",     "Sub01 2 Stim(SEB) CD154-VbetaResponsive D03 1", "Sub01 2 Stim(SEB) CD154-VbetaResponsive D04 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F01 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F06 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F08 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive G03 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive G07 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive H03 100",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive H04 100", "Sub02 1 Unstim VbetaResponsive A03 1",     "Sub02 1 Unstim VbetaResponsive A08 1", "Sub02 1 Unstim VbetaResponsive A10 1",     "Sub02 1 Unstim VbetaResponsive B04 1", "Sub02 1 Unstim VbetaResponsive B05 1",     "Sub02 1 Unstim VbetaResponsive B06 1", "Sub02 1 Unstim VbetaResponsive B08 1",     "Sub02 1 Unstim VbetaResponsive B10 1", "Sub02 1 Unstim VbetaResponsive B11 1",     "Sub02 1 Unstim VbetaResponsive C06 1", "Sub02 1 Unstim VbetaResponsive C08 1",     "Sub02 1 Unstim VbetaResponsive C09 1", "Sub02 1 Unstim VbetaResponsive C10 1",     "Sub02 1 Unstim VbetaResponsive C11 1", "Sub02 1 Unstim VbetaResponsive D03 1",     "Sub02 1 Unstim VbetaResponsive D05 1", "Sub02 1 Unstim VbetaResponsive D06 1",     "Sub02 1 Unstim VbetaResponsive D08 100", "Sub02 1 Unstim VbetaResponsive D09 100",     "Sub02 1 Unstim VbetaUnresponsive E03 1", "Sub02 1 Unstim VbetaUnresponsive E07 1",     "Sub02 1 Unstim VbetaUnresponsive E08 1", "Sub02 1 Unstim VbetaUnresponsive E12 1",     "Sub02 1 Unstim VbetaUnresponsive F02 1", "Sub02 1 Unstim VbetaUnresponsive F07 1",     "Sub02 1 Unstim VbetaUnresponsive F09 1", "Sub02 1 Unstim VbetaUnresponsive F10 1",     "Sub02 1 Unstim VbetaUnresponsive F11 1", "Sub02 1 Unstim VbetaUnresponsive G02 1",     "Sub02 1 Unstim VbetaUnresponsive G03 1", "Sub02 1 Unstim VbetaUnresponsive G04 1",     "Sub02 1 Unstim VbetaUnresponsive G07 1", "Sub02 1 Unstim VbetaUnresponsive G08 1",     "Sub02 1 Unstim VbetaUnresponsive G10 1", "Sub02 1 Unstim VbetaUnresponsive G12 1",     "Sub02 1 Unstim VbetaUnresponsive H02 1", "Sub02 1 Unstim VbetaUnresponsive H05 1",     "Sub02 1 Unstim VbetaUnresponsive H08 100", "Sub02 1 Unstim VbetaUnresponsive H09 100",     "Sub02 1 Unstim VbetaUnresponsive H10 100", "Sub02 1 Unstim VbetaUnresponsive H11 100",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A03 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive A05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A07 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive A10 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive B05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive B06 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive B11 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive B12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive C05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive C06 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive C10 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive C12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive D01 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive D08 100", "Sub02 2 Stim(SEB) CD154+VbetaResponsive D09 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E01 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E05 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E07 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E11 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F02 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F04 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F09 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G02 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G04 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G06 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H02 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H08 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H09 100", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H10 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H11 100", "Sub02 3 Stim(SEB) VbetaResponsive A03 1",     "Sub02 3 Stim(SEB) VbetaResponsive A05 1", "Sub02 3 Stim(SEB) VbetaResponsive A06 1",     "Sub02 3 Stim(SEB) VbetaResponsive A08 1", "Sub02 3 Stim(SEB) VbetaResponsive A11 1",     "Sub02 3 Stim(SEB) VbetaResponsive B01 1", "Sub02 3 Stim(SEB) VbetaResponsive B05 1",     "Sub02 3 Stim(SEB) VbetaResponsive B06 1", "Sub02 3 Stim(SEB) VbetaResponsive B07 1",     "Sub02 3 Stim(SEB) VbetaResponsive B11 1", "Sub02 3 Stim(SEB) VbetaResponsive C04 1",     "Sub02 3 Stim(SEB) VbetaResponsive C06 1", "Sub02 3 Stim(SEB) VbetaResponsive C10 1",     "Sub02 3 Stim(SEB) VbetaResponsive C11 1", "Sub02 3 Stim(SEB) VbetaResponsive C12 1",     "Sub02 3 Stim(SEB) VbetaResponsive D03 1", "Sub02 3 Stim(SEB) VbetaResponsive D04 1",     "Sub02 3 Stim(SEB) VbetaResponsive D05 1", "Sub02 3 Stim(SEB) VbetaResponsive D08 100",     "Sub02 3 Stim(SEB) VbetaResponsive D09 100", "Sub02 3 Stim(SEB) VbetaResponsive D10 100",     "Sub02 3 Stim(SEB) VbetaResponsive D11 100", "Sub02 3 Stim(SEB) VbetaUnresponsive E02 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive E06 1", "Sub02 3 Stim(SEB) VbetaUnresponsive E10 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F02 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F05 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F06 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F07 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F09 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F12 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G03 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G05 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G07 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G08 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G09 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G12 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive H01 1", "Sub02 3 Stim(SEB) VbetaUnresponsive H06 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive H08 100", "Sub02 3 Stim(SEB) VbetaUnresponsive H09 100",     "Sub02 3 Stim(SEB) VbetaUnresponsive H10 100", "Sub02 3 Stim(SEB) VbetaUnresponsive H11 100"    )), 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), 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 = 175L, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")],     n = nrow(X), list(X = X)))
 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0,     control = lmerControl(), ...) {    p <- ncol(X)    rho <- new.env(parent = parent.env(environment()))    rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta",         "Lambdat", "Lind")], n = nrow(X), list(X = X)))    REMLpass <- if (REML)         p    else 0L    rho$resp <- if (missing(fr))         mkRespMod(REML = REMLpass, ...)    else mkRespMod(fr, REML = REMLpass)    pp <- resp <- NULL    rho$lmer_Deviance <- lmer_Deviance    devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(),         resp$ptr(), as.double(theta))    environment(devfun) <- rho    if (is.null(start) && all(reTrms$cnms == "(Intercept)") &&         length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) {        v <- sapply(reTrms$flist, function(f) var(ave(y, f)))        v.e <- var(y) - sum(v)        if (!is.na(v.e) && v.e > 0) {            v.rel <- v/v.e            if (all(v.rel >= reTrms$lower^2))                 rho$pp$setTheta(sqrt(v.rel))        }    }    if (length(rho$resp$y) > 0)         devfun(rho$pp$theta)    rho$lower <- reTrms$lower    devfun})(fr = list(response = c(17.1549488, 17.96523889, 17.91863365, 18.36682488, 21.71978922, 22.28720095, 22.24042665, 21.8394648, 22.00848592, 22.557772, 22.82166197, 22.55326015, 22.75158998, 17.0307196, 17.24898821, 17.28722661, 18.77447611, 15.26442367, 18.33376099, 17.13877899, 17.22848628, 18.15424476, 17.7664056, 21.85570882, 22.16897842, 22.036942, 18.16295093, 18.3734392, 17.75490292, 16.67664086, 15.50248452, 21.98530514, 22.48662628, 21.86926882, 22.70824704, 22.25372624, 22.76834477, 17.56812314, 18.97171038, 15.48477938, 16.83122006, 18.50447634, 16.33141399, 16.98687939, 18.30138365, 17.21464373, 18.15005098, 22.50898504, 17.66227338, 17.9165828, 17.73275396, 17.96919195, 16.59547485, 17.8991097, 16.95919233, 18.46071303, 18.1430014, 17.33427817, 22.36632522, 22.65836318, 17.58852327, 18.04310748, 16.9768996, 15.89917816, 17.12385739, 16.54667389, 18.07982847, 17.33560142, 12.3145558, 18.4235911, 19.04598783, 17.35984444, 16.07742193, 17.59565246, 16.45933055, 16.87716167, 16.57776395, 23.28512305, 22.63358165, 16.55911522, 18.13480816, 17.54782997, 16.63357157, 17.22217855, 18.16120503, 16.3143401, 17.52568682, 16.69247442, 17.96974988, 17.34888362, 17.2607571, 17.30128452, 14.43549348, 17.89927349, 17.58699981, 17.09019156, 14.65166115, 22.74266939, 22.84638997, 23.18575911, 22.24542232, 17.27946053, 16.84244984, 17.68388379, 17.33027924, 18.84473748, 15.64092647, 18.67140162, 16.59336688, 21.76136685, 18.10274492, 18.86899898, 18.2627199, 16.36714198, 16.28637667, 22.99508549, 22.49469828, 17.8256644, 17.46763236, 15.46209421, 17.42237837, 17.38378116, 16.97711266, 17.16751018, 17.59929602, 17.29489375, 17.86035477, 17.01138283, 23.37640426, 23.23701073, 23.82367946, 23.10470336, 18.27915897, 17.58630168, 19.56432613, 18.57191446, 19.08620254, 16.43157369, 17.8017602, 17.31125532, 17.21175927, 16.518024, 17.1687239, 16.89736375, 17.14124302, 19.24149782, 17.18839622, 16.53831226, 17.35770757, 17.64899947, 23.00964636, 23.49809773, 23.50300131, 23.29289891, 19.16830962, 16.58899569, 18.03448075, 19.27309937, 17.68007615, 17.10023142, 18.7194558, 15.91092705, 18.03842259, 16.10158826, 17.37501075, 18.67434424, 17.8364885, 16.70124775, 17.54203635, 17.2817816, 17.92954623, 23.64260711, 23.31658008, 23.14526946, 23.49269212), `(Intercept)` = 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), Stim.ConditionUnstim = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Subject.ID = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L)), 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), reTrms = list(Zt = new("dgCMatrix",     i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), p = 0:175,     Dim = c(2L, 175L), Dimnames = list(c("Sub01", "Sub02"), c("Sub01 1 Stim(SEB) CD154+VbetaResponsive A10 1",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive B02 1", "Sub01 1 Stim(SEB) CD154+VbetaResponsive B06 1",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive B08 1", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H05 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H06 100", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H07 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H08 100", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H09 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H10 100", "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive G11 100",     "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive G12 100", "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive H01 100",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive B09 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive B11 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive B12 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C01 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C03 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C05 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C07 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C09 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C10 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive D01 1",     "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H02 100", "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H03 100",     "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H04 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive A01 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive A02 1", "Sub01 2 Stim(SEB) CD154+VbetaResponsive A08 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive A12 1", "Sub01 2 Stim(SEB) CD154+VbetaResponsive B07 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H05 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H06 100",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H07 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H08 100",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H09 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H10 100",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D06 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D09 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D11 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E01 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E02 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E05 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E06 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E07 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E10 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E11 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive G11 100", "Sub01 2 Stim(SEB) CD154-VbetaResponsive B12 1",     "Sub01 2 Stim(SEB) CD154-VbetaResponsive C05 1", "Sub01 2 Stim(SEB) CD154-VbetaResponsive C09 1",     "Sub01 2 Stim(SEB) CD154-VbetaResponsive D03 1", "Sub01 2 Stim(SEB) CD154-VbetaResponsive D04 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F01 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F06 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F08 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive G03 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive G07 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive H03 100",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive H04 100", "Sub02 1 Unstim VbetaResponsive A03 1",     "Sub02 1 Unstim VbetaResponsive A08 1", "Sub02 1 Unstim VbetaResponsive A10 1",     "Sub02 1 Unstim VbetaResponsive B04 1", "Sub02 1 Unstim VbetaResponsive B05 1",     "Sub02 1 Unstim VbetaResponsive B06 1", "Sub02 1 Unstim VbetaResponsive B08 1",     "Sub02 1 Unstim VbetaResponsive B10 1", "Sub02 1 Unstim VbetaResponsive B11 1",     "Sub02 1 Unstim VbetaResponsive C06 1", "Sub02 1 Unstim VbetaResponsive C08 1",     "Sub02 1 Unstim VbetaResponsive C09 1", "Sub02 1 Unstim VbetaResponsive C10 1",     "Sub02 1 Unstim VbetaResponsive C11 1", "Sub02 1 Unstim VbetaResponsive D03 1",     "Sub02 1 Unstim VbetaResponsive D05 1", "Sub02 1 Unstim VbetaResponsive D06 1",     "Sub02 1 Unstim VbetaResponsive D08 100", "Sub02 1 Unstim VbetaResponsive D09 100",     "Sub02 1 Unstim VbetaUnresponsive E03 1", "Sub02 1 Unstim VbetaUnresponsive E07 1",     "Sub02 1 Unstim VbetaUnresponsive E08 1", "Sub02 1 Unstim VbetaUnresponsive E12 1",     "Sub02 1 Unstim VbetaUnresponsive F02 1", "Sub02 1 Unstim VbetaUnresponsive F07 1",     "Sub02 1 Unstim VbetaUnresponsive F09 1", "Sub02 1 Unstim VbetaUnresponsive F10 1",     "Sub02 1 Unstim VbetaUnresponsive F11 1", "Sub02 1 Unstim VbetaUnresponsive G02 1",     "Sub02 1 Unstim VbetaUnresponsive G03 1", "Sub02 1 Unstim VbetaUnresponsive G04 1",     "Sub02 1 Unstim VbetaUnresponsive G07 1", "Sub02 1 Unstim VbetaUnresponsive G08 1",     "Sub02 1 Unstim VbetaUnresponsive G10 1", "Sub02 1 Unstim VbetaUnresponsive G12 1",     "Sub02 1 Unstim VbetaUnresponsive H02 1", "Sub02 1 Unstim VbetaUnresponsive H05 1",     "Sub02 1 Unstim VbetaUnresponsive H08 100", "Sub02 1 Unstim VbetaUnresponsive H09 100",     "Sub02 1 Unstim VbetaUnresponsive H10 100", "Sub02 1 Unstim VbetaUnresponsive H11 100",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A03 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive A05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A07 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive A10 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive B05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive B06 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive B11 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive B12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive C05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive C06 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive C10 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive C12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive D01 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive D08 100", "Sub02 2 Stim(SEB) CD154+VbetaResponsive D09 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E01 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E05 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E07 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E11 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F02 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F04 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F09 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G02 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G04 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G06 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H02 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H08 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H09 100", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H10 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H11 100", "Sub02 3 Stim(SEB) VbetaResponsive A03 1",     "Sub02 3 Stim(SEB) VbetaResponsive A05 1", "Sub02 3 Stim(SEB) VbetaResponsive A06 1",     "Sub02 3 Stim(SEB) VbetaResponsive A08 1", "Sub02 3 Stim(SEB) VbetaResponsive A11 1",     "Sub02 3 Stim(SEB) VbetaResponsive B01 1", "Sub02 3 Stim(SEB) VbetaResponsive B05 1",     "Sub02 3 Stim(SEB) VbetaResponsive B06 1", "Sub02 3 Stim(SEB) VbetaResponsive B07 1",     "Sub02 3 Stim(SEB) VbetaResponsive B11 1", "Sub02 3 Stim(SEB) VbetaResponsive C04 1",     "Sub02 3 Stim(SEB) VbetaResponsive C06 1", "Sub02 3 Stim(SEB) VbetaResponsive C10 1",     "Sub02 3 Stim(SEB) VbetaResponsive C11 1", "Sub02 3 Stim(SEB) VbetaResponsive C12 1",     "Sub02 3 Stim(SEB) VbetaResponsive D03 1", "Sub02 3 Stim(SEB) VbetaResponsive D04 1",     "Sub02 3 Stim(SEB) VbetaResponsive D05 1", "Sub02 3 Stim(SEB) VbetaResponsive D08 100",     "Sub02 3 Stim(SEB) VbetaResponsive D09 100", "Sub02 3 Stim(SEB) VbetaResponsive D10 100",     "Sub02 3 Stim(SEB) VbetaResponsive D11 100", "Sub02 3 Stim(SEB) VbetaUnresponsive E02 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive E06 1", "Sub02 3 Stim(SEB) VbetaUnresponsive E10 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F02 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F05 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F06 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F07 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F09 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F12 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G03 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G05 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G07 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G08 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G09 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G12 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive H01 1", "Sub02 3 Stim(SEB) VbetaUnresponsive H06 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive H08 100", "Sub02 3 Stim(SEB) VbetaUnresponsive H09 100",     "Sub02 3 Stim(SEB) VbetaUnresponsive H10 100", "Sub02 3 Stim(SEB) VbetaUnresponsive H11 100"    )), 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), 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(Subject.ID = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L)), cnms = list(    Subject.ID = "(Intercept)"), Ztlist = list(`1 | Subject.ID` = new("dgCMatrix",     i = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), p = 0:175,     Dim = c(2L, 175L), Dimnames = list(c("Sub01", "Sub02"), c("Sub01 1 Stim(SEB) CD154+VbetaResponsive A10 1",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive B02 1", "Sub01 1 Stim(SEB) CD154+VbetaResponsive B06 1",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive B08 1", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H05 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H06 100", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H07 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H08 100", "Sub01 1 Stim(SEB) CD154+VbetaResponsive H09 100",     "Sub01 1 Stim(SEB) CD154+VbetaResponsive H10 100", "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive G11 100",     "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive G12 100", "Sub01 1 Stim(SEB) CD154+VbetaUnresponsive H01 100",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive B09 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive B11 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive B12 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C01 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C03 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C05 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C07 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive C09 1",     "Sub01 1 Stim(SEB) CD154-VbetaResponsive C10 1", "Sub01 1 Stim(SEB) CD154-VbetaResponsive D01 1",     "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H02 100", "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H03 100",     "Sub01 1 Stim(SEB) CD154-VbetaUnresponsive H04 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive A01 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive A02 1", "Sub01 2 Stim(SEB) CD154+VbetaResponsive A08 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive A12 1", "Sub01 2 Stim(SEB) CD154+VbetaResponsive B07 1",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H05 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H06 100",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H07 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H08 100",     "Sub01 2 Stim(SEB) CD154+VbetaResponsive H09 100", "Sub01 2 Stim(SEB) CD154+VbetaResponsive H10 100",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D06 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D09 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive D11 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E01 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E02 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E05 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E06 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E07 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E10 1", "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive E11 1",     "Sub01 2 Stim(SEB) CD154+VbetaUnresponsive G11 100", "Sub01 2 Stim(SEB) CD154-VbetaResponsive B12 1",     "Sub01 2 Stim(SEB) CD154-VbetaResponsive C05 1", "Sub01 2 Stim(SEB) CD154-VbetaResponsive C09 1",     "Sub01 2 Stim(SEB) CD154-VbetaResponsive D03 1", "Sub01 2 Stim(SEB) CD154-VbetaResponsive D04 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F01 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F06 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive F08 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive G03 1",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive G07 1", "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive H03 100",     "Sub01 2 Stim(SEB) CD154-VbetaUnresponsive H04 100", "Sub02 1 Unstim VbetaResponsive A03 1",     "Sub02 1 Unstim VbetaResponsive A08 1", "Sub02 1 Unstim VbetaResponsive A10 1",     "Sub02 1 Unstim VbetaResponsive B04 1", "Sub02 1 Unstim VbetaResponsive B05 1",     "Sub02 1 Unstim VbetaResponsive B06 1", "Sub02 1 Unstim VbetaResponsive B08 1",     "Sub02 1 Unstim VbetaResponsive B10 1", "Sub02 1 Unstim VbetaResponsive B11 1",     "Sub02 1 Unstim VbetaResponsive C06 1", "Sub02 1 Unstim VbetaResponsive C08 1",     "Sub02 1 Unstim VbetaResponsive C09 1", "Sub02 1 Unstim VbetaResponsive C10 1",     "Sub02 1 Unstim VbetaResponsive C11 1", "Sub02 1 Unstim VbetaResponsive D03 1",     "Sub02 1 Unstim VbetaResponsive D05 1", "Sub02 1 Unstim VbetaResponsive D06 1",     "Sub02 1 Unstim VbetaResponsive D08 100", "Sub02 1 Unstim VbetaResponsive D09 100",     "Sub02 1 Unstim VbetaUnresponsive E03 1", "Sub02 1 Unstim VbetaUnresponsive E07 1",     "Sub02 1 Unstim VbetaUnresponsive E08 1", "Sub02 1 Unstim VbetaUnresponsive E12 1",     "Sub02 1 Unstim VbetaUnresponsive F02 1", "Sub02 1 Unstim VbetaUnresponsive F07 1",     "Sub02 1 Unstim VbetaUnresponsive F09 1", "Sub02 1 Unstim VbetaUnresponsive F10 1",     "Sub02 1 Unstim VbetaUnresponsive F11 1", "Sub02 1 Unstim VbetaUnresponsive G02 1",     "Sub02 1 Unstim VbetaUnresponsive G03 1", "Sub02 1 Unstim VbetaUnresponsive G04 1",     "Sub02 1 Unstim VbetaUnresponsive G07 1", "Sub02 1 Unstim VbetaUnresponsive G08 1",     "Sub02 1 Unstim VbetaUnresponsive G10 1", "Sub02 1 Unstim VbetaUnresponsive G12 1",     "Sub02 1 Unstim VbetaUnresponsive H02 1", "Sub02 1 Unstim VbetaUnresponsive H05 1",     "Sub02 1 Unstim VbetaUnresponsive H08 100", "Sub02 1 Unstim VbetaUnresponsive H09 100",     "Sub02 1 Unstim VbetaUnresponsive H10 100", "Sub02 1 Unstim VbetaUnresponsive H11 100",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A03 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive A05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A07 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive A10 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive A12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive B05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive B06 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive B11 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive B12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive C05 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive C06 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive C10 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive C12 1", "Sub02 2 Stim(SEB) CD154+VbetaResponsive D01 1",     "Sub02 2 Stim(SEB) CD154+VbetaResponsive D08 100", "Sub02 2 Stim(SEB) CD154+VbetaResponsive D09 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E01 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E05 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E07 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive E11 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F02 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F04 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive F09 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G02 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G04 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive G06 1",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H02 1", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H08 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H09 100", "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H10 100",     "Sub02 2 Stim(SEB) CD154-VbetaUnresponsive H11 100", "Sub02 3 Stim(SEB) VbetaResponsive A03 1",     "Sub02 3 Stim(SEB) VbetaResponsive A05 1", "Sub02 3 Stim(SEB) VbetaResponsive A06 1",     "Sub02 3 Stim(SEB) VbetaResponsive A08 1", "Sub02 3 Stim(SEB) VbetaResponsive A11 1",     "Sub02 3 Stim(SEB) VbetaResponsive B01 1", "Sub02 3 Stim(SEB) VbetaResponsive B05 1",     "Sub02 3 Stim(SEB) VbetaResponsive B06 1", "Sub02 3 Stim(SEB) VbetaResponsive B07 1",     "Sub02 3 Stim(SEB) VbetaResponsive B11 1", "Sub02 3 Stim(SEB) VbetaResponsive C04 1",     "Sub02 3 Stim(SEB) VbetaResponsive C06 1", "Sub02 3 Stim(SEB) VbetaResponsive C10 1",     "Sub02 3 Stim(SEB) VbetaResponsive C11 1", "Sub02 3 Stim(SEB) VbetaResponsive C12 1",     "Sub02 3 Stim(SEB) VbetaResponsive D03 1", "Sub02 3 Stim(SEB) VbetaResponsive D04 1",     "Sub02 3 Stim(SEB) VbetaResponsive D05 1", "Sub02 3 Stim(SEB) VbetaResponsive D08 100",     "Sub02 3 Stim(SEB) VbetaResponsive D09 100", "Sub02 3 Stim(SEB) VbetaResponsive D10 100",     "Sub02 3 Stim(SEB) VbetaResponsive D11 100", "Sub02 3 Stim(SEB) VbetaUnresponsive E02 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive E06 1", "Sub02 3 Stim(SEB) VbetaUnresponsive E10 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F02 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F05 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F06 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F07 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive F09 1", "Sub02 3 Stim(SEB) VbetaUnresponsive F12 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G03 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G05 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G07 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G08 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive G09 1", "Sub02 3 Stim(SEB) VbetaUnresponsive G12 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive H01 1", "Sub02 3 Stim(SEB) VbetaUnresponsive H06 1",     "Sub02 3 Stim(SEB) VbetaUnresponsive H08 100", "Sub02 3 Stim(SEB) VbetaUnresponsive H09 100",     "Sub02 3 Stim(SEB) VbetaUnresponsive H10 100", "Sub02 3 Stim(SEB) VbetaUnresponsive H11 100"    )), 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), factors = list())), nl = c(Subject.ID = 2L)),     REML = FALSE, 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 = "ignore", tol = 1e-04), check.conv.hess = list(            action = "warning", tol = 1e-06)), optCtrl = list()))
10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose,     control = control)))
11: (function (formula, data = NULL, REML = TRUE, control = lmerControl(),     start = NULL, verbose = 0L, subset, weights, na.action, offset,     contrasts = NULL, devFunOnly = FALSE) {    mc <- mcout <- match.call()    missCtrl <- missing(control)    if (!missCtrl && !inherits(control, "lmerControl")) {        if (!is.list(control))             stop("'control' is not a list; use lmerControl()")        warning("passing control as list is deprecated: please use lmerControl() instead",             immediate. = TRUE)        control <- do.call(lmerControl, control)    }    mc$control <- control    mc[[1]] <- quote(lme4::lFormula)    lmod <- eval(mc, parent.frame(1L))    mcout$formula <- lmod$formula    lmod$formula <- NULL    if (is.matrix(y <- model.response(lmod$fr)) && ncol(y) >         1) {        stop("can't handle matrix-valued responses: consider using refit()")    }    devfun <- do.call(mkLmerDevfun, c(lmod, list(start = start,         verbose = verbose, control = control)))    if (devFunOnly)         return(devfun)    if (identical(control$optimizer, "none"))         stop("deprecated use of optimizer=='none'; use NULL instead")    opt <- if (length(control$optimizer) == 0) {        s <- getStart(start, environment(devfun)$pp)        list(par = s, fval = devfun(s), conv = 1000, message = "no optimization")    }    else {        optimizeLmer(devfun, optimizer = control$optimizer, restart_edge = control$restart_edge,             boundary.tol = control$boundary.tol, control = control$optCtrl,             verbose = verbose, start = start, calc.derivs = control$calc.derivs,             use.last.params = control$use.last.params)    }    cc <- checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,         lbound = environment(devfun)$lower)    mkMerMod(environment(devfun), opt, lmod$reTrms, fr = lmod$fr,         mc = mcout, lme4conv = cc)})(formula = response ~ 0 + `(Intercept)` + Stim.ConditionUnstim +     (1 | Subject.ID), data = datpos, REML = FALSE, 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 = "ignore", tol = 1e-04), check.conv.hess = list(        action = "warning", tol = 1e-06)), optCtrl = list()))
12: do.call(cfun, c(list(formula = formC, data = quote(datpos)),     fitArgsC))
13: do.call(cfun, c(list(formula = formC, data = quote(datpos)),     fitArgsC))
14: .local(object, response = response, ...)
15: fit(object, silent = silent, start = start, ...)
16: fit(object, silent = silent, start = start, ...)
17: .local(object, response, ...)
18: fit(obj, response = t(assay(fd))[, 2])
19: fit(obj, response = t(assay(fd))[, 2])
20: eval(code, test_env)
21: eval(code, test_env)
22: 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)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: 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) {    })
30: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
31: source_file(path, env = env(env), desc = desc, error_call = error_call)
32: FUN(X[[i]], ...)
33: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
38: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
39: 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)
40: 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)
41: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
42: test_check("MAST")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)

Example timings

MAST.Rcheck/MAST-Ex.timings

nameusersystemelapsed
Drop0.0010.0000.000
FromFlatDF0.7860.0360.775
FromMatrix0.2600.0280.288
Hypothesis0.0070.0000.007
LRT0.1160.0440.150
ZlmFit-class1.5440.0521.596
applyFlat0.0010.0000.002
bootVcov10.6440.0480.693
calcZ1.0780.0121.091
collectResiduals1.6900.0281.718
computeEtFromCt0.0380.0080.045
convertMASTClassicToSingleCellAssay0.3250.0040.329
defaultAssay0.0410.0000.041
defaultPrior0.0000.0010.001
expavg0.0000.0010.000
filterLowExpressedGenes0.2450.0020.247
freq0.0330.0000.033
getConcordance0.4560.0560.498
getwellKey0.0110.0080.020
gseaAfterBoot1.1660.0441.210
hushWarning0.0000.0000.001
impute1.2800.0321.313
invlogit000
logFC0.3520.0360.387
logmean0.0000.0000.001
lrTest0.7710.0360.808
mast_filter1.1990.0081.207
meld_list_left0.0010.0000.002
melt.SingleCellAssay0.4890.0080.485
new_with_repaired_slots0.0070.0000.008
plot.thresholdSCRNACountMatrix0.4610.0590.521
plotSCAConcordance0.8250.0010.798
predict.ZlmFit1.2940.0121.307
se.coef1.5840.1081.693
split-SingleCellAssay-character-method0.9020.0040.906
stat_ell1.0570.0241.081
subset-SingleCellAssay-method0.2400.0000.239
summary-GSEATests-method1.0700.0361.107
summary-ZlmFit-method0.4740.0080.483
thresholdSCRNACountMatrix0.3750.0160.391
waldTest0.7340.0080.742
zlm0.3860.0000.387