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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:alabaster.matrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings alabaster.matrix_0.99.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/alabaster.matrix.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.matrix/DESCRIPTION’ ... OK
* this is package ‘alabaster.matrix’ version ‘0.99.1’
* 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
* 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 R 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 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 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: writeSparseMatrix
> ### Title: Write a sparse matrix
> ### Aliases: writeSparseMatrix
> 
> ### ** Examples
> 
> library(Matrix)
> x <- rsparsematrix(100, 20, 0.5)
> tmp <- tempfile(fileext=".h5")
> writeSparseMatrix(x, tmp, "csc_matrix")
The 'cset' argument has been deprecated.
Please use the argument 'encoding' instead.
The 'cset' argument has been deprecated.
Please use the argument 'encoding' instead.
> writeSparseMatrix(x, tmp, "csr_matrix", column=FALSE)
The 'cset' argument has been deprecated.
Please use the argument 'encoding' instead.
The 'cset' argument has been deprecated.
Please use the argument 'encoding' instead.
Error in H5Dset_extent(did, dims) : HDF5. Dataset. Can't set value.
Calls: writeSparseMatrix ... .blockwise_sparse_writer -> h5set_extent -> H5Dset_extent
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:
    1. ├─alabaster.base::stageObject(x, dir, file.path(experiment, assay)) at test-stage-matrix.R:142:4
    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.         └─alabaster.matrix:::.stage_sparse_matrix(x, dir, path, child = child)
    7.           └─alabaster.matrix::writeSparseMatrix(...)
    8.             └─alabaster.matrix:::.write_CS_matrix(...)
    9.               └─alabaster.matrix:::.blockwise_sparse_writer(...)
   10.                 └─rhdf5::h5set_extent(file, iname, newlast)
   11.                   └─rhdf5::H5Dset_extent(did, dims)
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 49 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘userguide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/alabaster.matrix.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL alabaster.matrix
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘alabaster.matrix’ ...
** using staged installation
** R
** 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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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)
> test_check("alabaster.matrix")
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 49 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sparse.R:17:9'): writing to a sparse matrix works as expected ──
Error in `H5Dset_extent(did, dims)`: HDF5. Dataset. Can't set value.
Backtrace:
    ▆
 1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csr_matrix", column = FALSE) at test-sparse.R:17:8
 2.   └─alabaster.matrix:::.write_CS_matrix(...)
 3.     └─alabaster.matrix:::.blockwise_sparse_writer(...)
 4.       └─rhdf5::h5set_extent(file, iname, newlast)
 5.         └─rhdf5::H5Dset_extent(did, dims)
── Error ('test-sparse.R:32:5'): writing to a sparse matrix works with tiny chunks ──
Error in `setAutoBlockSize(max(dim(x)) * 8)`: could not find function "setAutoBlockSize"
── Error ('test-sparse.R:67:9'): writing to a sparse matrix works with guessed type ──
Error in `H5Dopen(fhandle, path)`: could not find function "H5Dopen"
Backtrace:
    ▆
 1. ├─testthat::expect_match(get_type(tmp, "csc_matrix/data"), "I32") at test-sparse.R:67:8
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─alabaster.matrix (local) get_type(tmp, "csc_matrix/data")
── Error ('test-sparse.R:104:9'): writing to a sparse matrix works with guessed index type for block method ──
Error in `H5Dopen(fhandle, path)`: could not find function "H5Dopen"
Backtrace:
    ▆
 1. ├─testthat::expect_match(get_type(tmp, "csc_matrix/indices"), "U16") at test-sparse.R:104:8
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─alabaster.matrix (local) get_type(tmp, "csc_matrix/indices")
── Error ('test-stage-matrix.R:123:5'): stageObject works with logical matrices ──
Error in `H5Dset_extent(did, dims)`: HDF5. Dataset. Can't set value.
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(mat, dir, file.path(experiment, assay2)) at test-stage-matrix.R:123:4
  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:::.blockwise_sparse_writer(...)
  9.               └─rhdf5::h5set_extent(file, iname, newlast)
 10.                 └─rhdf5::H5Dset_extent(did, dims)
── Error ('test-stage-matrix.R:142:5'): stageObject works with DelayedMatrices (naive) ──
Error in `H5Dset_extent(did, dims)`: HDF5. Dataset. Can't set value.
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(x, dir, file.path(experiment, assay)) at test-stage-matrix.R:142:4
  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.         └─alabaster.matrix:::.stage_sparse_matrix(x, dir, path, child = child)
  7.           └─alabaster.matrix::writeSparseMatrix(...)
  8.             └─alabaster.matrix:::.write_CS_matrix(...)
  9.               └─alabaster.matrix:::.blockwise_sparse_writer(...)
 10.                 └─rhdf5::h5set_extent(file, iname, newlast)
 11.                   └─rhdf5::H5Dset_extent(did, dims)

[ FAIL 6 | WARN 0 | SKIP 0 | PASS 49 ]
Error: Test failures
Execution halted