Multiple platform build/check report for BioC 3.20 - BUILD results for HiContacts on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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 HiContacts on taishan

To the developers/maintainers of the HiContacts package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiContacts.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: HiContacts

Version: 1.8.0

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

StartedAt: 2025-04-01 00:10:30 -0000 (Tue, 01 Apr 2025)

EndedAt: 2025-04-01 00:13:45 -0000 (Tue, 01 Apr 2025)

EllapsedTime: 195.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiContacts
###
##############################################################################
##############################################################################


* checking for file ‘HiContacts/DESCRIPTION’ ... OK
* preparing ‘HiContacts’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HiContacts.Rmd’ using rmarkdown
Warning in for (i in seq_len(n)) { :
  closing unused connection 4 (/home/biocbuild/.cache/R/ExperimentHub/37cbb2193e94e6_7751)

Quitting from HiContacts.Rmd:120-127 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'con' in selecting a method for function 'import': HDF5. File accessibility. Unable to open file.
---
Backtrace:
     ▆
  1. ├─BiocIO::import(...)
  2. ├─BiocIO::import(...)
  3. │ ├─BiocIO::import(FileForFormat(con, format), ...)
  4. │ └─BiocIO::FileForFormat(con, format)
  5. │   └─get(constructorName, ns)(path)
  6. │     └─HiCExperiment:::.check_cool_file(path)
  7. │       └─HiCExperiment:::.is_cool(path)
  8. │         └─HiCExperiment:::.lsCoolFiles(path)
  9. │           ├─(function(x) {...
 10. │           │ └─base::gsub("//", "/", x)
 11. │           │   └─base::is.factor(x)
 12. │           ├─base::unique(...)
 13. │           ├─dplyr::pull(...)
 14. │           ├─dplyr::mutate(rhdf5::h5ls(file), path = paste0(group, "/", name))
 15. │           └─rhdf5::h5ls(file)
 16. │             └─rhdf5:::h5checktypeOrOpenLoc(...)
 17. │               └─rhdf5::H5Fopen(file, flags = flags, fapl = fapl, native = native)
 18. └─base::.handleSimpleError(...)
 19.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'HiContacts.Rmd' failed with diagnostics:
error in evaluating the argument 'con' in selecting a method for function 'import': HDF5. File accessibility. Unable to open file.
--- failed re-building ‘HiContacts.Rmd’

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

Error: Vignette re-building failed.
Execution halted