Multiple platform build/check report for BioC 3.22 - BUILD results for SparseArray on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for SparseArray on taishan

To the developers/maintainers of the SparseArray package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SparseArray.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: SparseArray

Version: 1.9.1

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SparseArray

StartedAt: 2025-10-21 03:19:47 -0000 (Tue, 21 Oct 2025)

EndedAt: 2025-10-21 03:21:02 -0000 (Tue, 21 Oct 2025)

EllapsedTime: 75.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SparseArray
###
##############################################################################
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* checking for file ‘SparseArray/DESCRIPTION’ ... OK
* preparing ‘SparseArray’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SparseArray_objects.Rmd’ using rmarkdown

Quitting from SparseArray_objects.Rmd:450-456 [unnamed-chunk-30]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `rhdf5::H5Fopen()`:
! HDF5. File accessibility. Unable to open file.
---
Backtrace:
    ▆
 1. └─HDF5Array::TENxMatrix(hub[["EH1039"]], group = "mm10")
 2.   └─HDF5Array::TENxMatrixSeed(filepath, group)
 3.     └─HDF5Array::H5SparseMatrixSeed(filepath, group)
 4.       └─HDF5Array:::.check_group(filepath, group)
 5.         └─h5mread::h5exists(filepath, group)
 6.           └─h5mread:::.H5Fopen(filepath, flags = "H5F_ACC_RDONLY")
 7.             ├─base::suppressMessages(rhdf5::H5Fopen(name, flags = flags, fapl = fapl))
 8.             │ └─base::withCallingHandlers(...)
 9.             └─rhdf5::H5Fopen(name, flags = flags, fapl = fapl)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SparseArray_objects.Rmd' failed with diagnostics:
HDF5. File accessibility. Unable to open file.
--- failed re-building ‘SparseArray_objects.Rmd’

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

Error: Vignette re-building failed.
Execution halted