##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:alabaster.matrix.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings alabaster.matrix_1.5.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'alabaster.matrix/DESCRIPTION' ... OK
* this is package 'alabaster.matrix' version '1.5.4'
* 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 whether package 'alabaster.matrix' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... 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 ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/alabaster.matrix/libs/x64/alabaster.matrix.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'alabaster.matrix-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: saveDelayedArray
> ### Title: Save DelayedArrays to disk
> ### Aliases: saveDelayedArray stageObject,DelayedArray-method
> ###   stageObject,DelayedMatrix-method saveObject,DelayedArray-method
> 
> ### ** Examples
> 
> mat <- Matrix::rsparsematrix(100, 200, density=0.2)
> rownames(mat) <- paste0("GENE_", seq_len(nrow(mat)))
> dmat <- DelayedArray::DelayedArray(mat) * 1
> 
> dir <- tempfile()
> saveObject(dmat, dir, delayed.preserve.ops=TRUE)
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Execution halted
* 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:
    9.             └─alabaster.matrix:::.extract_sparse_details(mat)
   10.               └─DelayedArray::blockApply(...)
   11.                 └─DelayedArray::gridApply(...)
   12.                   └─S4Arrays:::bplapply2(...)
   13.                     ├─BiocGenerics::lapply(X, FUN, ...)
   14.                     └─base::lapply(X, FUN, ...)
   15.                       └─DelayedArray (local) FUN(X[[i]], ...)
   16.                         └─DelayedArray (local) FUN(viewport, ...)
   17.                           └─alabaster.matrix (local) FUN(block, ...)
   18.                             └─SparseArray::nzdata(sparse)
   19.                               └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  
  [ FAIL 13 | WARN 90 | SKIP 0 | PASS 558 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL alabaster.matrix
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'alabaster.matrix' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c collect_attributes.cpp -o collect_attributes.o
g++ -std=gnu++17 -shared -s -static-libgcc -o alabaster.matrix.dll tmp.def RcppExports.o collect_attributes.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-alabaster.matrix/00new/alabaster.matrix/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (alabaster.matrix)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
[ FAIL 13 | WARN 90 | SKIP 0 | PASS 558 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-AmalgamatedArray.R:52:5'): Amalgamated staging and loading works when the inner arrays are delayed wrappers ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(mat, temp, "amalgam") at test-AmalgamatedArray.R:52:5
  2. └─alabaster.matrix::stageObject(mat, temp, "amalgam")
  3.   └─alabaster.matrix (local) .local(x, dir, path, child, ...)
  4.     └─alabaster.base::.stageObject(...)
  5.       └─alabaster.base::altStageObject(...)
  6.         ├─alabaster.base (local) FUN(...)
  7.         └─alabaster.matrix (local) FUN(...)
  8.           └─alabaster.matrix (local) .local(x, dir, path, child, ...)
  9.             └─alabaster.matrix:::.stage_delayed(...)
 10.               └─alabaster.matrix (local) fallback(x, dir, path, child = child)
 11.                 └─alabaster.matrix:::.stage_sparse_matrix(x, dir, path, child = child)
 12.                   └─alabaster.matrix::writeSparseMatrix(...)
 13.                     └─alabaster.matrix:::.write_CS_matrix(...)
 14.                       ├─alabaster.matrix:::.extract_sparse_details(mat)
 15.                       └─alabaster.matrix:::.extract_sparse_details(mat)
 16.                         ├─alabaster.matrix:::.extract_sparse_details(x@seed)
 17.                         └─alabaster.matrix:::.extract_sparse_details(x@seed)
 18.                           └─DelayedArray::blockApply(...)
 19.                             └─DelayedArray::gridApply(...)
 20.                               └─S4Arrays:::bplapply2(...)
 21.                                 ├─BiocGenerics::lapply(X, FUN, ...)
 22.                                 └─base::lapply(X, FUN, ...)
 23.                                   └─DelayedArray (local) FUN(X[[i]], ...)
 24.                                     └─DelayedArray (local) FUN(viewport, ...)
 25.                                       └─alabaster.matrix (local) FUN(block, ...)
 26.                                         └─SparseArray::nzdata(sparse)
 27.                                           └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-SparseMatrix.R:53:13'): writing to a sparse matrix works as expected for numeric data ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:53:13
  2. └─alabaster.matrix::saveObject(x, tmp)
  3.   └─alabaster.matrix (local) .local(x, path, ...)
  4.     └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...)
  5.       └─alabaster.matrix:::optimize_storage(x)
  6.         └─alabaster.matrix:::optimize_float_storage(x)
  7.           ├─alabaster.matrix:::collect_float_attributes(x)
  8.           └─alabaster.matrix:::collect_float_attributes(x)
  9.             └─DelayedArray::blockApply(...)
 10.               └─DelayedArray::gridApply(...)
 11.                 └─S4Arrays:::bplapply2(...)
 12.                   ├─BiocGenerics::lapply(X, FUN, ...)
 13.                   └─base::lapply(X, FUN, ...)
 14.                     └─DelayedArray (local) FUN(X[[i]], ...)
 15.                       └─DelayedArray (local) FUN(viewport, ...)
 16.                         └─alabaster.matrix (local) FUN(block, ...)
 17.                           └─SparseArray::nzdata(y)
 18.                             └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-SparseMatrix.R:77:13'): writing to a sparse matrix works as expected for logical data ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:77:13
  2. └─alabaster.matrix::saveObject(x, tmp)
  3.   └─alabaster.matrix (local) .local(x, path, ...)
  4.     └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...)
  5.       └─alabaster.matrix:::optimize_storage(x)
  6.         └─alabaster.matrix:::optimize_boolean_storage(x)
  7.           ├─alabaster.matrix:::collect_boolean_attributes(x)
  8.           └─alabaster.matrix:::collect_boolean_attributes(x)
  9.             └─DelayedArray::blockApply(...)
 10.               └─DelayedArray::gridApply(...)
 11.                 └─S4Arrays:::bplapply2(...)
 12.                   ├─BiocGenerics::lapply(X, FUN, ...)
 13.                   └─base::lapply(X, FUN, ...)
 14.                     └─DelayedArray (local) FUN(X[[i]], ...)
 15.                       └─DelayedArray (local) FUN(viewport, ...)
 16.                         └─alabaster.matrix (local) FUN(block, ...)
 17.                           └─SparseArray::nzdata(x)
 18.                             └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-SparseMatrix.R:100:13'): writing to a sparse matrix works as expected for integer data ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:100:13
  2. └─alabaster.matrix::saveObject(x, tmp)
  3.   └─alabaster.matrix (local) .local(x, path, ...)
  4.     └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...)
  5.       └─alabaster.matrix:::optimize_storage(x)
  6.         └─alabaster.matrix:::optimize_integer_storage(x)
  7.           ├─alabaster.matrix:::collect_integer_attributes(x)
  8.           └─alabaster.matrix:::collect_integer_attributes(x)
  9.             └─DelayedArray::blockApply(...)
 10.               └─DelayedArray::gridApply(...)
 11.                 └─S4Arrays:::bplapply2(...)
 12.                   ├─BiocGenerics::lapply(X, FUN, ...)
 13.                   └─base::lapply(X, FUN, ...)
 14.                     └─DelayedArray (local) FUN(X[[i]], ...)
 15.                       └─DelayedArray (local) FUN(viewport, ...)
 16.                         └─alabaster.matrix (local) FUN(block, ...)
 17.                           ├─alabaster.matrix:::.simple_integer_collector(nzdata(y))
 18.                           │ └─base::suppressWarnings(range(x, na.rm = TRUE))
 19.                           │   └─base::withCallingHandlers(...)
 20.                           └─SparseArray::nzdata(y)
 21.                             └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-SparseMatrix.R:138:9'): depositing small chunks works correctly ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. └─base::eval(...)
  2.   └─base::eval(...)
  3.     ├─alabaster.base::saveObject(y, tmp) at test-SparseMatrix.R:138:9
  4.     └─alabaster.matrix::saveObject(y, tmp)
  5.       └─alabaster.matrix (local) .local(x, path, ...)
  6.         └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...)
  7.           └─alabaster.matrix:::optimize_storage(x)
  8.             └─alabaster.matrix:::optimize_float_storage(x)
  9.               ├─alabaster.matrix:::collect_float_attributes(x)
 10.               └─alabaster.matrix:::collect_float_attributes(x)
 11.                 └─DelayedArray::blockApply(...)
 12.                   └─DelayedArray::gridApply(...)
 13.                     └─S4Arrays:::bplapply2(...)
 14.                       ├─BiocGenerics::lapply(X, FUN, ...)
 15.                       └─base::lapply(X, FUN, ...)
 16.                         └─DelayedArray (local) FUN(X[[i]], ...)
 17.                           └─DelayedArray (local) FUN(viewport, ...)
 18.                             └─alabaster.matrix (local) FUN(block, ...)
 19.                               └─SparseArray::nzdata(y)
 20.                                 └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-SparseMatrix.R:174:9'): fallback to large integer types for indices works correctly ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:174:9
  2. └─alabaster.matrix::saveObject(x, tmp)
  3.   └─alabaster.matrix (local) .local(x, path, ...)
  4.     └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...)
  5.       └─alabaster.matrix:::optimize_storage(x)
  6.         └─alabaster.matrix:::optimize_float_storage(x)
  7.           ├─alabaster.matrix:::collect_float_attributes(x)
  8.           └─alabaster.matrix:::collect_float_attributes(x)
  9.             └─DelayedArray::blockApply(...)
 10.               └─DelayedArray::gridApply(...)
 11.                 └─S4Arrays:::bplapply2(...)
 12.                   ├─BiocGenerics::lapply(X, FUN, ...)
 13.                   └─base::lapply(X, FUN, ...)
 14.                     └─DelayedArray (local) FUN(X[[i]], ...)
 15.                       └─DelayedArray (local) FUN(viewport, ...)
 16.                         └─alabaster.matrix (local) FUN(block, ...)
 17.                           └─SparseArray::nzdata(y)
 18.                             └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-SparseMatrix.R:224:5'): writing a DelayedMatrixworks with row-major storage ──
Error in `.Call2(.NAME, ..., PACKAGE = "SparseArray")`: 'x' must be a [d|l|n]gCMatrix object
Backtrace:
     ▆
  1. ├─alabaster.base::saveObject(y, tmp) at test-SparseMatrix.R:224:5
  2. └─alabaster.matrix::saveObject(y, tmp)
  3.   └─alabaster.matrix (local) .local(x, path, ...)
  4.     └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...)
  5.       └─alabaster.matrix:::optimize_storage(x)
  6.         └─alabaster.matrix:::optimize_float_storage(x)
  7.           ├─alabaster.matrix:::collect_float_attributes(x)
  8.           └─alabaster.matrix:::collect_float_attributes(x)
  9.             └─DelayedArray::blockApply(...)
 10.               └─DelayedArray::gridApply(...)
 11.                 └─S4Arrays:::bplapply2(...)
 12.                   ├─BiocGenerics::lapply(X, FUN, ...)
 13.                   └─base::lapply(X, FUN, ...)
 14.                     └─DelayedArray (local) FUN(X[[i]], ...)
 15.                       └─DelayedArray (local) FUN(viewport, ...)
 16.                         └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
 17.                           └─S4Arrays:::.NEW_read_block(x, viewport, as.sparse = as.sparse)
 18.                             ├─SparseArray::read_block_as_sparse(x, viewport)
 19.                             └─SparseArray::read_block_as_sparse(x, viewport)
 20.                               ├─SparseArray::extract_sparse_array(x, Nindex)
 21.                               └─DelayedArray::extract_sparse_array(x, Nindex)
 22.                                 ├─SparseArray::extract_sparse_array(x@seed, index)
 23.                                 └─DelayedArray::extract_sparse_array(x@seed, index)
 24.                                   ├─SparseArray::extract_sparse_array(x@seed, index)
 25.                                   └─SparseArray::extract_sparse_array(x@seed, index)
 26.                                     └─methods::as(slice, "SparseArray")
 27.                                       └─SparseArray (local) asMethod(object)
 28.                                         └─methods::as(from, "SVT_SparseArray")
 29.                                           └─SparseArray (local) asMethod(object)
 30.                                             └─methods::as(from, "SVT_SparseMatrix")
 31.                                               └─SparseArray (local) asMethod(object)
 32.                                                 └─SparseArray:::.build_SVT_SparseMatrix_from_CsparseMatrix(from)
 33.                                                   └─SparseArray:::SparseArray.Call(...)
 34.                                                     └─S4Vectors::.Call2(.NAME, ..., PACKAGE = "SparseArray")
── Error ('test-optimize_storage.R:422:14'): storage optimization works for sparse objects ──
<notSubsettableError/error/condition>
Error in `.Primitive("[")(new("SparseArraySeed", dim = c(100L, 10L), nzindex = structure(c(1L, 
24L, 57L, 67L, 76L, 82L, 98L, 10L, 34L, 37L, 41L, 42L, 55L, 64L, 
72L, 80L, 84L, 89L, 90L, 91L, 7L, 10L, 18L, 33L, 39L, 41L, 54L, 
55L, 56L, 59L, 96L, 99L, 8L, 19L, 29L, 32L, 43L, 44L, 45L, 60L, 
65L, 67L, 81L, 82L, 86L, 3L, 17L, 19L, 28L, 31L, 48L, 64L, 65L, 
94L, 99L, 7L, 21L, 47L, 58L, 65L, 68L, 76L, 77L, 100L, 8L, 12L, 
28L, 32L, 39L, 57L, 59L, 69L, 75L, 77L, 87L, 10L, 39L, 46L, 54L, 
68L, 74L, 100L, 5L, 15L, 29L, 34L, 61L, 66L, 73L, 75L, 97L, 100L, 
6L, 15L, 19L, 27L, 32L, 40L, 77L, 85L, 94L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 
9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 
10L, 10L), dim = c(101L, 2L)), nzdata = c(NA, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 
10000L, 10000L), dimnames = list(NULL, NULL)), 1:10, , drop = FALSE)`: object of type 'S4' is not subsettable
Backtrace:
     ▆
  1. └─alabaster.matrix:::optimize_storage(fun(y)) at test-optimize_storage.R:422:14
  2.   └─alabaster.matrix:::optimize_integer_storage(x)
  3.     ├─alabaster.matrix:::collect_integer_attributes(x)
  4.     └─alabaster.matrix:::collect_integer_attributes(x)
  5.       └─DelayedArray::blockApply(...)
  6.         └─DelayedArray::gridApply(...)
  7.           └─S4Arrays:::bplapply2(...)
  8.             ├─BiocGenerics::lapply(X, FUN, ...)
  9.             └─base::lapply(X, FUN, ...)
 10.               └─DelayedArray (local) FUN(X[[i]], ...)
 11.                 └─DelayedArray (local) FUN(viewport, ...)
 12.                   └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
 13.                     └─S4Arrays:::.NEW_read_block(x, viewport, as.sparse = as.sparse)
 14.                       ├─SparseArray::read_block_as_sparse(x, viewport)
 15.                       └─SparseArray::read_block_as_sparse(x, viewport)
 16.                         ├─SparseArray::extract_sparse_array(x, Nindex)
 17.                         └─DelayedArray::extract_sparse_array(x, Nindex)
 18.                           ├─SparseArray::extract_sparse_array(x@seed, index)
 19.                           └─SparseArray::extract_sparse_array(x@seed, index)
 20.                             └─S4Arrays:::subset_by_Nindex(x, index)
 21.                               ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
 22.                               └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
── Error ('test-sparse.R:21:9'): writing to a sparse matrix works as expected ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:21:9
  2.   └─alabaster.matrix:::.write_CS_matrix(...)
  3.     ├─alabaster.matrix:::.extract_sparse_details(mat)
  4.     └─alabaster.matrix:::.extract_sparse_details(mat)
  5.       ├─alabaster.matrix:::.extract_sparse_details(x@seed)
  6.       └─alabaster.matrix:::.extract_sparse_details(x@seed)
  7.         └─DelayedArray::blockApply(...)
  8.           └─DelayedArray::gridApply(...)
  9.             └─S4Arrays:::bplapply2(...)
 10.               ├─BiocGenerics::lapply(X, FUN, ...)
 11.               └─base::lapply(X, FUN, ...)
 12.                 └─DelayedArray (local) FUN(X[[i]], ...)
 13.                   └─DelayedArray (local) FUN(viewport, ...)
 14.                     └─alabaster.matrix (local) FUN(block, ...)
 15.                       └─SparseArray::nzdata(sparse)
 16.                         └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-sparse.R:47:9'): writing to a sparse matrix works with tiny chunks ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:47:9
  2.   └─alabaster.matrix:::.write_CS_matrix(...)
  3.     ├─alabaster.matrix:::.extract_sparse_details(mat)
  4.     └─alabaster.matrix:::.extract_sparse_details(mat)
  5.       ├─alabaster.matrix:::.extract_sparse_details(x@seed)
  6.       └─alabaster.matrix:::.extract_sparse_details(x@seed)
  7.         └─DelayedArray::blockApply(...)
  8.           └─DelayedArray::gridApply(...)
  9.             └─S4Arrays:::bplapply2(...)
 10.               ├─BiocGenerics::lapply(X, FUN, ...)
 11.               └─base::lapply(X, FUN, ...)
 12.                 └─DelayedArray (local) FUN(X[[i]], ...)
 13.                   └─DelayedArray (local) FUN(viewport, ...)
 14.                     └─alabaster.matrix (local) FUN(block, ...)
 15.                       └─SparseArray::nzdata(sparse)
 16.                         └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-sparse.R:87:9'): writing to a sparse matrix works with guessed type ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. └─alabaster.matrix::writeSparseMatrix(y, tmp, "csc_matrix") at test-sparse.R:87:9
  2.   └─alabaster.matrix:::.write_CS_matrix(...)
  3.     ├─alabaster.matrix:::.extract_sparse_details(mat)
  4.     └─alabaster.matrix:::.extract_sparse_details(mat)
  5.       ├─alabaster.matrix:::.extract_sparse_details(x@seed)
  6.       └─alabaster.matrix:::.extract_sparse_details(x@seed)
  7.         └─DelayedArray::blockApply(...)
  8.           └─DelayedArray::gridApply(...)
  9.             └─S4Arrays:::bplapply2(...)
 10.               ├─BiocGenerics::lapply(X, FUN, ...)
 11.               └─base::lapply(X, FUN, ...)
 12.                 └─DelayedArray (local) FUN(X[[i]], ...)
 13.                   └─DelayedArray (local) FUN(viewport, ...)
 14.                     └─alabaster.matrix (local) FUN(block, ...)
 15.                       └─SparseArray::nzdata(sparse)
 16.                         └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-sparse.R:128:13'): writing to a sparse matrix works with guessed index type for block method ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:128:13
  2.   └─alabaster.matrix:::.write_CS_matrix(...)
  3.     ├─alabaster.matrix:::.extract_sparse_details(mat)
  4.     └─alabaster.matrix:::.extract_sparse_details(mat)
  5.       ├─alabaster.matrix:::.extract_sparse_details(x@seed)
  6.       └─alabaster.matrix:::.extract_sparse_details(x@seed)
  7.         └─DelayedArray::blockApply(...)
  8.           └─DelayedArray::gridApply(...)
  9.             └─S4Arrays:::bplapply2(...)
 10.               ├─BiocGenerics::lapply(X, FUN, ...)
 11.               └─base::lapply(X, FUN, ...)
 12.                 └─DelayedArray (local) FUN(X[[i]], ...)
 13.                   └─DelayedArray (local) FUN(viewport, ...)
 14.                     └─alabaster.matrix (local) FUN(block, ...)
 15.                       └─SparseArray::nzdata(sparse)
 16.                         └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-stage-matrix.R:123:5'): stageObject works with logical matrices ──
Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"'
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(mat, dir, file.path(experiment, assay2)) at test-stage-matrix.R:123:5
  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.         └─alabaster.matrix::writeSparseMatrix(...)
  7.           └─alabaster.matrix:::.write_CS_matrix(...)
  8.             ├─alabaster.matrix:::.extract_sparse_details(mat)
  9.             └─alabaster.matrix:::.extract_sparse_details(mat)
 10.               └─DelayedArray::blockApply(...)
 11.                 └─DelayedArray::gridApply(...)
 12.                   └─S4Arrays:::bplapply2(...)
 13.                     ├─BiocGenerics::lapply(X, FUN, ...)
 14.                     └─base::lapply(X, FUN, ...)
 15.                       └─DelayedArray (local) FUN(X[[i]], ...)
 16.                         └─DelayedArray (local) FUN(viewport, ...)
 17.                           └─alabaster.matrix (local) FUN(block, ...)
 18.                             └─SparseArray::nzdata(sparse)
 19.                               └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)

[ FAIL 13 | WARN 90 | SKIP 0 | PASS 558 ]
Error: Test failures
Execution halted