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###
### Running command:
###
###   _R_CHECK_CODETOOLS_PROFILE_="suppressFundefMismatch=TRUE" /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings DelayedArray_0.33.6.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedArray.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DelayedArray/DESCRIPTION’ ... OK
* this is package ‘DelayedArray’ version ‘0.33.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'stats4', 'Matrix', 'BiocGenerics', 'MatrixGenerics', 'S4Vectors',
  'IRanges', 'S4Arrays', 'SparseArray'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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:
  .BBSoptions
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 ‘DelayedArray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DelayedArray-utils.Rd: arbind, acbind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘defaultMultAutoGrids’
Undocumented S4 methods:
  generic '[' and siglist 'DelayedArray,ANY,ANY,ANY'
  generic '[<-' and siglist 'DelayedArray,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DelayedArray-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DelayedArray-stats
> ### Title: Statistical functions on DelayedArray objects
> ### Aliases: DelayedArray-stats dnorm dnorm,DelayedArray-method pnorm
> ###   pnorm,DelayedArray-method qnorm qnorm,DelayedArray-method dbinom
> ###   dbinom,DelayedArray-method pbinom pbinom,DelayedArray-method qbinom
> ###   qbinom,DelayedArray-method dpois dpois,DelayedArray-method ppois
> ###   ppois,DelayedArray-method qpois qpois,DelayedArray-method dlogis
> ###   dlogis,DelayedArray-method plogis plogis,DelayedArray-method qlogis
> ###   qlogis,DelayedArray-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> a <- array(4 * runif(1500000), dim=c(10000, 30, 5))
> A <- DelayedArray(a)
> A
<10000 x 30 x 5> DelayedArray object of type "double":
,,1
              [,1]      [,2]      [,3] ...     [,29]     [,30]
    [1,] 1.0620347 0.2588500 0.8424110   .  2.393853  1.456900
    [2,] 1.4884956 2.7064496 0.4591455   .  1.530954  1.207247
     ...         .         .         .   .         .         .
 [9999,] 2.2724650 2.4062400 0.2929517   . 1.8491122 2.0628324
[10000,] 2.6107082 0.4452701 1.3654351   . 0.4947538 1.4261293

...

,,5
              [,1]      [,2]      [,3] ...     [,29]     [,30]
    [1,] 2.1651764 0.1518611 1.6980807   . 3.4377479 3.9473490
    [2,] 2.4254841 1.6660715 1.0479329   . 0.2056194 1.2510120
     ...         .         .         .   .         .         .
 [9999,] 1.8211024 1.5312842 0.2665814   .  2.821739  1.098839
[10000,] 1.8941378 2.8878833 2.3148489   .  3.121096  3.422325

> 
> A2 <- dnorm(A + 1)[ , , -3]  # very fast! (operations are delayed)
> A2
<10000 x 30 x 4> DelayedArray object of type "double":
,,1
                 [,1]         [,2]         [,3] ...       [,29]       [,30]
    [1,] 0.0475995492 0.1806325970 0.0730816734   . 0.001258221 0.019504381
    [2,] 0.0180385579 0.0004147549 0.1375880299   . 0.016215269 0.034912577
     ...            .            .            .   .           .           .
 [9999,] 0.0018857079 0.0012063282 0.1729417231   . 0.006890176 0.003663231
[10000,] 0.0005887286 0.1403885547 0.0243169878   . 0.130539042 0.021026112

...

,,4
                [,1]        [,2]        [,3] ...        [,29]        [,30]
    [1,] 0.002663513 0.205495617 0.010475058   . 2.111046e-05 1.931778e-06
    [2,] 0.001129580 0.011414085 0.048999115   . 1.928780e-01 3.166745e-02
     ...           .           .           .   .            .            .
 [9999,] 0.007459641 0.016201712 0.178877727   . 2.687360e-04 4.409091e-02
[10000,] 0.006054489 0.000208253 0.001640014   . 8.184727e-05 2.260320e-05

> 
> a2 <- as.array(A2)           # "realize" 'A2' in memory (as an ordinary
>                              # array)
> 
> DelayedArray(a2) == A2       # DelayedArray object of type "logical"
<10000 x 30 x 4> DelayedArray object of type "logical":
,,1
          [,1]  [,2]  [,3] ... [,29] [,30]
    [1,]  TRUE  TRUE  TRUE   .  TRUE  TRUE
    [2,]  TRUE  TRUE  TRUE   .  TRUE  TRUE
     ...     .     .     .   .     .     .
 [9999,]  TRUE  TRUE  TRUE   .  TRUE  TRUE
[10000,]  TRUE  TRUE  TRUE   .  TRUE  TRUE

...

,,4
          [,1]  [,2]  [,3] ... [,29] [,30]
    [1,]  TRUE  TRUE  TRUE   .  TRUE  TRUE
    [2,]  TRUE  TRUE  TRUE   .  TRUE  TRUE
     ...     .     .     .   .     .     .
 [9999,]  TRUE  TRUE  TRUE   .  TRUE  TRUE
[10000,]  TRUE  TRUE  TRUE   .  TRUE  TRUE

> stopifnot(all(DelayedArray(a2) == A2))
> 
> 
> library(HDF5Array)
Loading required package: h5mread
Loading required package: rhdf5

Attaching package: ‘h5mread’

The following object is masked from ‘package:rhdf5’:

    h5ls

> A3 <- as(A2, "HDF5Array")    # "realize" 'A2' on disk (as an HDF5Array
Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
Error in H5Fclose(file$H5Identifier) : 
  HDF5. Object cache. Internal error detected.
Calls: as ... h5write -> h5write.default -> h5closeitLoc -> H5Fclose
Execution halted

 *** caught segfault ***
address 0x558, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
DelayedArray-class 5.485  0.195   6.087
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  17: BLOCK_rowsum(m1, group1, reorder = reorder, na.rm = na.rm, grid = grid1,     as.sparse = NA, BPPARAM = NULL, BACKEND = "HDF5Array")
  18: func()
  19: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
  20: doTryCatch(return(expr), name, parentenv, handler)
  21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  22: tryCatchList(expr, classes, parentenv, handlers)
  23: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
  24: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
  25: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp,     tearDownFunc = .tearDown)
  26: .sourceTestFile(testFile, testSuite$testFuncRegexp)
  27: RUnit::runTestSuite(suite)
  28: BiocGenerics:::testPackage("DelayedArray")
  29: DelayedArray:::.test()
  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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedArray.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL DelayedArray
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘DelayedArray’ ...
** this is package ‘DelayedArray’ version ‘0.33.6’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_DelayedArray.c -o R_init_DelayedArray.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c compress_atomic_vector.c -o compress_atomic_vector.o
gcc -shared -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-DelayedArray/00new/DelayedArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a new generic function for ‘sweep’ in package ‘DelayedArray’
Creating a new generic function for ‘scale’ in package ‘DelayedArray’
Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DelayedArray)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> require("DelayedArray") || stop("unable to load DelayedArray package")
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

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: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

[1] TRUE
> DelayedArray:::.test()
Error in S4Arrays:::normarg_perm(perm, dim(seed)) : 
  'perm' must be an integer vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    'perm' cannot be an empty vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions with an extent of 1 can be dropped
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    all non-NA values in 'perm' must be >= 1 and <= 'length(dim(a))'
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions with an extent of 1 can be dropped
Loading required package: h5mread
Loading required package: rhdf5

Attaching package: 'h5mread'

The following object is masked from 'package:rhdf5':

    h5ls

Timing stopped at: 0.54 0.028 0.572
Error in H5Fclose(file$H5Identifier) : 
  HDF5. Object cache. Internal error detected.
In addition: Warning messages:
1: In log(a + 0.2) : NaNs produced
2: In OP(a) : NaNs produced

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: H5Fget_name(x)
 2: FUN(X[[i]], ...)
 3: lapply(X = X, FUN = FUN, ...)
 4: sapply(L[which(isobject)], function(x) {    H5Fget_name(x) == filename})
 5: h5FileIsOpen(file)
 6: h5checktypeOrOpenLoc(file, native = native)
 7: h5createDataset(filepath, name, dim, maxdims = maxdim, storage.mode = type,     H5type = H5type, size = size, chunk = chunkdim, level = level)
 8: h5createDataset2(filepath, name, dim, maxdim = maxdim, type = type,     H5type = H5type, size = size, chunkdim = chunkdim, level = level)
 9: create_and_log_HDF5_dataset(filepath, name, dim, type = type,     H5type = H5type, size = size, chunkdim = chunkdim, level = level)
10: (function (dim, dimnames = NULL, type = "double", as.sparse = FALSE,     filepath = NULL, name = NULL, H5type = NULL, size = NULL,     chunkdim = NULL, level = NULL) {    if (!isTRUEorFALSE(as.sparse))         stop(wmsg("'as.sparse' must be TRUE or FALSE"))    if (is.null(filepath)) {        filepath <- getHDF5DumpFile()    }    else {        filepath <- normalize_dump_filepath(filepath)    }    if (is.null(name)) {        name <- getHDF5DumpName(for.use = TRUE)    }    else {        name <- normalize_dump_name(name)    }    if (is.null(chunkdim)) {        chunkdim <- getHDF5DumpChunkDim(dim)    }    else if (isSingleNumber(chunkdim) && chunkdim == 0) {        chunkdim <- NULL    }    else {        chunkdim <- .normarg_chunkdim(chunkdim, dim)    }    if (is.null(level)) {        if (is.null(chunkdim)) {            level <- 0L        }        else {            level <- getHDF5DumpCompressionLevel()        }    }    else {        level <- normalize_compression_level(level)    }    create_and_log_HDF5_dataset(filepath, name, dim, type = type,         H5type = H5type, size = size, chunkdim = chunkdim, level = level)    if (is.null(dimnames)) {        dimnames <- vector("list", length(dim))    }    else {        h5writeDimnames(dimnames, filepath, name)    }    new2("HDF5RealizationSink", dim = dim, dimnames = dimnames,         type = type, as_sparse = as.sparse, filepath = filepath,         name = name, chunkdim = chunkdim)})(6:5, list(c("1", "2", "3", "4", "5", "6"), c("A", "B", "C", "D", "E")), "double", as.sparse = FALSE)
11: do.call(realization_sink_constructor, args)
12: do.call(realization_sink_constructor, args)
13: .AutoRealizationSink(...)
14: RealizationSink(BACKEND, refdim(sink_grid), dimnames = sink_dimnames,     type = "double", ...)
15: .make_shared_sink_along_vstrips(input_grid, sink_grid, BACKEND,     sink_rownames, sink_colnames, ...)
16: make_shared_sink_and_grid_along_vstrips(BPPARAM, grid, ans_dim[[1L]],     BACKEND, ugroup, colnames(x), ...)
17: BLOCK_rowsum(m1, group1, reorder = reorder, na.rm = na.rm, grid = grid1,     as.sparse = NA, BPPARAM = NULL, BACKEND = "HDF5Array")
18: func()
19: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
24: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
25: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp,     tearDownFunc = .tearDown)
26: .sourceTestFile(testFile, testSuite$testFuncRegexp)
27: RUnit::runTestSuite(suite)
28: BiocGenerics:::testPackage("DelayedArray")
29: DelayedArray:::.test()
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)