Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-27 11:36:56 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4436 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4461 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R 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 1148/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MAST 1.29.0 (landing page) Andrew McDavid
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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)
MAST.Rcheck/MAST-Ex.timings
name | user | system | elapsed | |
Drop | 0.001 | 0.000 | 0.000 | |
FromFlatDF | 0.786 | 0.036 | 0.775 | |
FromMatrix | 0.260 | 0.028 | 0.288 | |
Hypothesis | 0.007 | 0.000 | 0.007 | |
LRT | 0.116 | 0.044 | 0.150 | |
ZlmFit-class | 1.544 | 0.052 | 1.596 | |
applyFlat | 0.001 | 0.000 | 0.002 | |
bootVcov1 | 0.644 | 0.048 | 0.693 | |
calcZ | 1.078 | 0.012 | 1.091 | |
collectResiduals | 1.690 | 0.028 | 1.718 | |
computeEtFromCt | 0.038 | 0.008 | 0.045 | |
convertMASTClassicToSingleCellAssay | 0.325 | 0.004 | 0.329 | |
defaultAssay | 0.041 | 0.000 | 0.041 | |
defaultPrior | 0.000 | 0.001 | 0.001 | |
expavg | 0.000 | 0.001 | 0.000 | |
filterLowExpressedGenes | 0.245 | 0.002 | 0.247 | |
freq | 0.033 | 0.000 | 0.033 | |
getConcordance | 0.456 | 0.056 | 0.498 | |
getwellKey | 0.011 | 0.008 | 0.020 | |
gseaAfterBoot | 1.166 | 0.044 | 1.210 | |
hushWarning | 0.000 | 0.000 | 0.001 | |
impute | 1.280 | 0.032 | 1.313 | |
invlogit | 0 | 0 | 0 | |
logFC | 0.352 | 0.036 | 0.387 | |
logmean | 0.000 | 0.000 | 0.001 | |
lrTest | 0.771 | 0.036 | 0.808 | |
mast_filter | 1.199 | 0.008 | 1.207 | |
meld_list_left | 0.001 | 0.000 | 0.002 | |
melt.SingleCellAssay | 0.489 | 0.008 | 0.485 | |
new_with_repaired_slots | 0.007 | 0.000 | 0.008 | |
plot.thresholdSCRNACountMatrix | 0.461 | 0.059 | 0.521 | |
plotSCAConcordance | 0.825 | 0.001 | 0.798 | |
predict.ZlmFit | 1.294 | 0.012 | 1.307 | |
se.coef | 1.584 | 0.108 | 1.693 | |
split-SingleCellAssay-character-method | 0.902 | 0.004 | 0.906 | |
stat_ell | 1.057 | 0.024 | 1.081 | |
subset-SingleCellAssay-method | 0.240 | 0.000 | 0.239 | |
summary-GSEATests-method | 1.070 | 0.036 | 1.107 | |
summary-ZlmFit-method | 0.474 | 0.008 | 0.483 | |
thresholdSCRNACountMatrix | 0.375 | 0.016 | 0.391 | |
waldTest | 0.734 | 0.008 | 0.742 | |
zlm | 0.386 | 0.000 | 0.387 | |