##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:alabaster.matrix.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings alabaster.matrix_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/alabaster.matrix.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.matrix/DESCRIPTION’ ... OK
* this is package ‘alabaster.matrix’ version ‘1.11.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alabaster.matrix’ can be installed ... OK
* used C++ compiler: ‘g++ (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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: .onLoad failed in loadNamespace() for 'HDF5Array', details:
  call: .set_dump_dir(dir)
  error: cannot create directory "/tmp/RtmpkSQE9x/HDF5Array_dump"
Call sequence:
Execution halted
* 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 ... WARNING
NEWS.Rd: Sections \title, and \name must exist and be unique in Rd files
AmalgamatedArray.Rd: Sections \title, and \name must exist and be unique in Rd files
DelayedMask.Rd: Sections \title, and \name must exist and be unique in Rd files
ReloadedArraySeed.Rd: Sections \title, and \name must exist and be unique in Rd files
WrapperArraySeed.Rd: Sections \title, and \name must exist and be unique in Rd files
createRawArraySeed.Rd: Sections \title, and \name must exist and be unique in Rd files
preserveDelayedOperations.Rd: Sections \title, and \name must exist and be unique in Rd files
readArray.Rd: Sections \title, and \name must exist and be unique in Rd files
readDelayedArray.Rd: Sections \title, and \name must exist and be unique in Rd files
readSparseMatrix.Rd: Sections \title, and \name must exist and be unique in Rd files
recycleHdf5Files.Rd: Sections \title, and \name must exist and be unique in Rd files
saveArray.Rd: Sections \title, and \name must exist and be unique in Rd files
saveDelayedArray.Rd: Sections \title, and \name must exist and be unique in Rd files
saveSparseMatrix.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
writeSparseMatrix.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in ‘NEWS.Rd’, ‘AmalgamatedArray.Rd’, ‘DelayedMask.Rd’, ‘ReloadedArraySeed.Rd’, ‘WrapperArraySeed.Rd’, ‘createRawArraySeed.Rd’, ‘preserveDelayedOperations.Rd’, ‘readArray.Rd’, ‘readDelayedArray.Rd’, ‘readSparseMatrix.Rd’, ‘recycleHdf5Files.Rd’, ‘saveArray.Rd’, ‘saveDelayedArray.Rd’, ‘saveSparseMatrix.Rd’, ‘storeDelayedObject.Rd’, ‘writeSparseMatrix.Rd’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* 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:
   5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
   6.         └─base::write(...)
   7.           └─base::cat(...)
   8.             └─base::file(file, ifelse(append, "a", "w"))
  
  [ FAIL 43 | WARN 164 | SKIP 0 | PASS 559 ]
  > 
  > proc.time()
     user  system elapsed 
   49.704   1.225  50.916 
  
   *** caught segfault ***
  address 0x558, cause 'memory not mapped'
  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
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/alabaster.matrix.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL alabaster.matrix
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘alabaster.matrix’ ...
** this is package ‘alabaster.matrix’ version ‘1.11.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c collect_attributes.cpp -o collect_attributes.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o alabaster.matrix.so RcppExports.o collect_attributes.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-alabaster.matrix/00new/alabaster.matrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (alabaster.matrix)

R Under development (unstable) (2025-10-28 r88973) -- "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.

> library(testthat)
> library(alabaster.matrix)
Loading required package: alabaster.base
> test_check("alabaster.matrix")
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: 'matrixStats'

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

    anyMissing


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

Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
Saving _problems/test-sparse-128.R
Saving _problems/test-sparse-128.R
Saving _problems/test-sparse-142.R
Saving _problems/test-stage-array-19.R
Saving _problems/test-stage-array-39.R
Saving _problems/test-stage-array-83.R
Saving _problems/test-stage-array-102.R
Saving _problems/test-stage-array-129.R
Saving _problems/test-stage-array-143.R
Saving _problems/test-stage-array-186.R
Saving _problems/test-stage-array-239.R
Saving _problems/test-stage-matrix-16.R
Saving _problems/test-stage-matrix-37.R
Saving _problems/test-stage-matrix-58.R
Saving _problems/test-stage-matrix-95.R
Saving _problems/test-stage-matrix-111.R
Saving _problems/test-stage-matrix-142.R
Saving _problems/test-storeDelayedObject-26.R
Saving _problems/test-storeDelayedObject-51.R
Saving _problems/test-storeDelayedObject-58.R
Saving _problems/test-storeDelayedObject-86.R
Saving _problems/test-storeDelayedObject-113.R
Saving _problems/test-storeDelayedObject-120.R
Saving _problems/test-storeDelayedObject-137.R
Saving _problems/test-storeDelayedObject-154.R
Saving _problems/test-storeDelayedObject-183.R
Saving _problems/test-storeDelayedObject-192.R
Saving _problems/test-storeDelayedObject-207.R
Saving _problems/test-storeDelayedObject-219.R
Saving _problems/test-storeDelayedObject-230.R
Saving _problems/test-storeDelayedObject-243.R
Saving _problems/test-storeDelayedObject-254.R
Saving _problems/test-storeDelayedObject-268.R
Saving _problems/test-storeDelayedObject-603.R
Saving _problems/test-storeDelayedObject-615.R
Saving _problems/test-storeDelayedObject-645.R
Saving _problems/test-storeDelayedObject-655.R
Saving _problems/test-storeDelayedObject-665.R
Saving _problems/test-storeDelayedObject-681.R
Saving _problems/test-storeDelayedObject-693.R
Saving _problems/test-storeDelayedObject-771.R
Saving _problems/test-storeDelayedObject-780.R
Saving _problems/test-storeDelayedObject-795.R
[ FAIL 43 | WARN 164 | SKIP 0 | PASS 559 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sparse.R:128:13'): writing to a sparse matrix works with guessed index type for block method ──
Error in `H5Dclose(h5dataset)`: HDF5. Virtual File Layer. Write failed.
Backtrace:
    ▆
 1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:128:13
 2.   └─alabaster.matrix:::.write_CS_matrix(...)
 3.     ├─alabaster.matrix:::.dump_column_sparse_matrix(...)
 4.     └─alabaster.matrix:::.dump_column_sparse_matrix(...)
 5.       ├─rhdf5::h5writeDataset(transformer(x@x), handle, data.path)
 6.       └─rhdf5:::h5writeDataset.double(transformer(x@x), handle, data.path)
 7.         └─rhdf5:::h5writeDataset.array(...)
 8.           └─rhdf5::H5Dclose(h5dataset)
── Error ('test-sparse.R:128:13'): writing to a sparse matrix works with guessed index type for block method ──
Error in `H5Fclose(handle)`: HDF5. File accessibility. Unable to close file.
Backtrace:
    ▆
 1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:128:13
 2.   └─alabaster.matrix:::.write_CS_matrix(...)
 3.     └─rhdf5::H5Fclose(handle)
── Error ('test-sparse.R:142:9'): writing to a sparse matrix works with NA values ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:142:9
 2.   └─rhdf5::h5createFile(file)
 3.     └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:19:5'): stageObject works as expected for the default method ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(arr, dir, file.path(experiment, assay)) at test-stage-array.R:19:5
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:39:9'): stageObject works as expected for NA values ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(arr, dir, file.path(experiment, "assay-0")) at test-stage-array.R:39:9
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:83:5'): stageObject works as expected without dimnames ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(arr, dir, file.path(experiment, assay)) at test-stage-array.R:83:5
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:102:5'): stageObject works with DelayedArrays ────
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(x, dir, file.path(experiment, assay)) at test-stage-array.R:102:5
 2. └─alabaster.matrix::stageObject(x, dir, file.path(experiment, assay))
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_delayed(...)
 5.       └─alabaster.matrix (local) fallback(x, dir, path, child = child)
 6.         └─rhdf5::h5createFile(ofile)
 7.           └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:129:5'): stageObject works with DelayedArrays with preserved operations ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(x, dir, file.path(experiment, assay)) at test-stage-array.R:129:5
 2. └─alabaster.matrix::stageObject(x, dir, file.path(experiment, assay))
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_delayed(...)
 5.       └─chihaya::saveDelayed(x, file.path(dir, xpath), "data")
 6.         └─rhdf5::h5createFile(file)
 7.           └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:143:5'): stageObject works with DelayedArrays with local references ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(arr, dir, paste0(experiment, "/raw")) at test-stage-array.R:143:5
 2. └─alabaster.matrix::stageObject(arr, dir, paste0(experiment, "/raw"))
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:186:5'): stageObject recycles existing HDF5Arrays ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. └─methods::as(matrix(runif(1000), 10, 100), "HDF5Array") at test-stage-array.R:186:5
 2.   └─HDF5Array (local) asMethod(object)
 3.     └─HDF5Array::writeHDF5Array(from)
 4.       └─HDF5Array::HDF5RealizationSink(...)
 5.         └─HDF5Array::getHDF5DumpFile()
 6.           └─HDF5Array:::.get_dump_autofile()
 7.             └─rhdf5::h5createFile(filepath)
 8.               └─rhdf5::H5Fcreate(file)
── Error ('test-stage-array.R:239:9'): reading arrays work with non-default NA placeholders ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(x, dir, "dense") at test-stage-array.R:239:9
 2. └─alabaster.matrix::stageObject(x, dir, "dense")
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-matrix.R:16:5'): stageObject works as expected for the default method ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(mat, dir, file.path(experiment, assay)) at test-stage-matrix.R:16:5
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-matrix.R:37:5'): stageObject works as expected without dimnames ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(mat, dir, file.path(experiment, assay)) at test-stage-matrix.R:37:5
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-matrix.R:58:5'): stageObject works with sparse matrices ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(mat, dir, file.path(experiment, assay)) at test-stage-matrix.R:58:5
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_any_matrix(x, dir, path, child = child)
 5.       └─alabaster.matrix:::.stage_sparse_matrix(x, dir, path, child = child)
 6.         └─rhdf5::h5createFile(ofile)
 7.           └─rhdf5::H5Fcreate(file)
── Error ('test-stage-matrix.R:95:5'): stageObject works with character matrices and missing values ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(mat, dir, file.path(experiment, assay)) at test-stage-matrix.R:95:5
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-matrix.R:111:5'): stageObject works with logical matrices ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(...) at test-stage-matrix.R:111:5
 2. └─alabaster.matrix::stageObject(...)
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_array(x, dir, path, child = child)
 5.       └─rhdf5::h5createFile(ofile)
 6.         └─rhdf5::H5Fcreate(file)
── Error ('test-stage-matrix.R:142:5'): stageObject works with DelayedMatrices (naive) ──
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(x, dir, file.path(experiment, assay)) at test-stage-matrix.R:142:5
 2. └─alabaster.matrix::stageObject(x, dir, file.path(experiment, assay))
 3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.matrix:::.stage_delayed(...)
 5.       └─chihaya::saveDelayed(x, file.path(dir, xpath), "data")
 6.         └─rhdf5::h5createFile(file)
 7.           └─rhdf5::H5Fcreate(file)
── Error ('test-storeDelayedObject.R:26:5'): ConstantArrays are saved correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X) at test-storeDelayedObject.R:26:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:51:5'): ConstantArrays are still saved correctly after some deep nesting ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:51:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:58:5'): ConstantArrays behave correctly with NAs ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X) at test-storeDelayedObject.R:58:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:86:5'): dense arrays are saved correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X) at test-storeDelayedObject.R:86:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:113:5'): dense array saving handles dimnames ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(DelayedArray(X)) at test-storeDelayedObject.R:113:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:120:5'): dense array saving handles a bit of transposition ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X) at test-storeDelayedObject.R:120:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:137:5'): dense arrays are saved to external arrays if requested ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X, DelayedArray.force.external = TRUE) at test-storeDelayedObject.R:137:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:154:5'): sparse matrices are saved correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X) at test-storeDelayedObject.R:154:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:183:5'): sparse matrix saving handles dimnames ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(DelayedArray(X)) at test-storeDelayedObject.R:183:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:192:5'): sparse matrices are saved to external arrays if requested ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(DelayedArray(X), DelayedArray.force.external = TRUE) at test-storeDelayedObject.R:192:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:207:5'): DelayedAbind works along rows ────
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:207:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:219:5'): DelayedAbind works along columns ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:219:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:230:5'): DelayedAbind works for 3D arrays ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:230:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:243:5'): DelayedAperm works along rows ────
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:243:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:254:5'): DelayedAperm works for 3D arrays ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:254:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:268:5'): DelayedNaryIsoOp works as expected (arithmetic) ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:268:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:603:5'): DelayedUnaryIsoOpWithArgs handles logical renaming ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:603:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:615:5'): DelayedUnaryIsoOpWithArgs handles NAs correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:615:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:645:5'): DelayedUnaryIsoOpWithArgs handles side-ness correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:645:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:655:5'): DelayedUnaryIsoOpWithArgs handles repeated operations correctly (same side) ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:655:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:665:5'): DelayedUnaryIsoOpWithArgs handles repeated operations correctly (opposite sides) ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(Z) at test-storeDelayedObject.R:665:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:681:5'): saving of a LowRankMatrix works correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(thing) at test-storeDelayedObject.R:681:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:693:5'): saving of a ResidualMatrix works correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(thing) at test-storeDelayedObject.R:693:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:771:5'): external saving handles seeds without saveObject methods ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X) at test-storeDelayedObject.R:771:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:780:5'): external saving avoids over-nesting of ReloadedArraySeed objects ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X) at test-storeDelayedObject.R:780:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-storeDelayedObject.R:795:5'): external deduplication is done correctly ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.matrix (local) saveDelayed(X, DelayedArray.force.external = TRUE, array.dedup.session = dedup.session) at test-storeDelayedObject.R:795:5
 2.   ├─alabaster.base::saveObject(...) at test-storeDelayedObject.R:9:5
 3.   └─alabaster.matrix::saveObject(...)
 4.     └─alabaster.matrix (local) .local(x, path, ...)
 5.       └─alabaster.base::saveObjectFile(path, "delayed_array", list(delayed_array = list(version = "1.0")))
 6.         └─base::write(...)
 7.           └─base::cat(...)
 8.             └─base::file(file, ifelse(append, "a", "w"))

[ FAIL 43 | WARN 164 | SKIP 0 | PASS 559 ]
> 
> proc.time()
   user  system elapsed 
 49.704   1.225  50.916 

 *** caught segfault ***
address 0x558, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)