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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings HDF5Array_1.35.16.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/HDF5Array.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 ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.35.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .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 ‘HDF5Array’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
* 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:
  H5SparseMatrix-class.Rd: h5ls
  H5SparseMatrixSeed-class.Rd: h5ls
  HDF5Array-class.Rd: H5File, h5ls
  HDF5ArraySeed-class.Rd: h5ls
  ReshapedHDF5Array-class.Rd: h5ls
  ReshapedHDF5ArraySeed-class.Rd: h5ls
  TENxMatrix-class.Rd: h5ls
  TENxMatrixSeed-class.Rd: h5ls
  dump-management.Rd: h5createDataset, h5ls
  writeHDF5Array.Rd: DelayedArray, h5writeDimnames, h5ls
  writeTENxMatrix.Rd: DelayedMatrix, h5ls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
TENxMatrix-class 48.517 12.596  41.132
writeTENxMatrix  12.321  0.678  13.373
HDF5Array-class   1.717  0.221   5.867
* 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:
  HDF5Array RUnit Tests - 5 test functions, 2 errors, 0 failures
  ERROR in test_CSR_H5ADMatrixSeed: Error : Error creating conda environment '/home/rapidbuild/.cache/R/basilisk/1.19.3/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' [exit code 1]
  ERROR in test_Dense_H5ADMatrixSeed: Error : Error creating conda environment '/home/rapidbuild/.cache/R/basilisk/1.19.3/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' [exit code 1]
  
  Test files with failing tests
  
     test_H5ADMatrixSeed-class.R 
       test_CSR_H5ADMatrixSeed 
       test_Dense_H5ADMatrixSeed 
  
  
  Error in BiocGenerics:::testPackage("HDF5Array") : 
    unit tests failed for package HDF5Array
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘HDF5Array_performance.Rmd’ using rmarkdown

Quitting from HDF5Array_performance.Rmd:355-358 [writeTENxMatrix_norm_brain1_s]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `H5Dclose()`:
! HDF5. Virtual File Layer. Write failed.
---
Backtrace:
     ▆
  1. ├─base::system.time(...)
  2. └─HDF5Array::writeTENxMatrix(norm_brain1_s, level = 0)
  3.   └─DelayedArray::BLOCK_write_to_sink(sink, x, verbose = verbose)
  4.     └─DelayedArray::sinkApply(...)
  5.       └─DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
  6.         └─DelayedArray (local) FUN(viewport, init, ...)
  7.           └─DelayedArray (local) FUN(init, viewport, ...)
  8.             ├─S4Arrays::write_block(sink, viewport, block)
  9.             └─HDF5Array::write_block(sink, viewport, block)
 10.               └─HDF5Array:::.append_data(sink@filepath, sink@group, block@nzdata)
 11.                 └─HDF5Array:::h5append(filepath, name, data)
 12.                   ├─rhdf5::h5write(data, filepath, name, start = old_len + 1, count = data_len)
 13.                   └─rhdf5:::h5write.default(...)
 14.                     ├─rhdf5::h5writeDataset(obj, loc$H5Identifier, name, ...)
 15.                     └─rhdf5:::h5writeDataset.double(obj, loc$H5Identifier, name, ...)
 16.                       └─rhdf5:::h5writeDataset.array(...)
 17.                         └─rhdf5::H5Dclose(h5dataset)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'HDF5Array_performance.Rmd' failed with diagnostics:
HDF5. Virtual File Layer. Write failed.
--- failed re-building ‘HDF5Array_performance.Rmd’

SUMMARY: processing the following file failed:
  ‘HDF5Array_performance.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/HDF5Array.Rcheck/00check.log’
for details.