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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HDF5Array_1.35.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HDF5Array.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.35.15’
* 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 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 31.523  6.196  20.733
writeTENxMatrix   9.721  0.457  10.400
* 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:
   
  FAILURE in test_Dense_H5ADMatrixSeed: Error in checkIdentical(dimnames(sce), dimnames(seed)) : FALSE 
   
  
  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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.