Multiple platform build/check report for BioC 3.21 - BUILD results for CuratedAtlasQueryR on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4581
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 CuratedAtlasQueryR on kunpeng2

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

Version: 1.6.0

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

StartedAt: 2025-09-16 06:00:46 -0000 (Tue, 16 Sep 2025)

EndedAt: 2025-09-16 06:38:13 -0000 (Tue, 16 Sep 2025)

EllapsedTime: 2246.5 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 CuratedAtlasQueryR
###
##############################################################################
##############################################################################


* checking for file ‘CuratedAtlasQueryR/DESCRIPTION’ ... OK
* preparing ‘CuratedAtlasQueryR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from Introduction.Rmd:218-254 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument '.data' in selecting a method for function 'join_features': ℹ In index: 1.
Caused by error in `value[[3L]]()`:
! File
  https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellxgene-0.2.1-hdf5/cpm/14583378cfb01c89f1a1fbb860f306dd/assays.h5
  could not be downloaded. Error in curl::curl_fetch_disk(url, x$path, handle =
  handle): Timeout was reached [object-store.rc.nectar.org.au]: Operation too
  slow. Less than 1 bytes/sec transferred the last 600 seconds
---
Backtrace:
     ▆
  1. ├─tibble::as_tibble(...)
  2. ├─tidySingleCellExperiment::join_features(...)
  3. ├─base::suppressMessages(...)
  4. │ └─base::withCallingHandlers(...)
  5. ├─CuratedAtlasQueryR::get_single_cell_experiment(...)
  6. │ └─CuratedAtlasQueryR:::sync_assay_files(...)
  7. │   └─purrr::pmap_chr(...)
  8. │     └─purrr:::pmap_("character", .l, .f, ..., .progress = .progress)
  9. │       ├─purrr:::with_indexed_errors(...)
 10. │       │ └─base::withCallingHandlers(...)
 11. │       ├─purrr:::call_with_cleanup(...)
 12. │       └─CuratedAtlasQueryR (local) .f(...)
 13. │         └─CuratedAtlasQueryR:::sync_remote_file(full_url, output_file)
 14. │           └─base::tryCatch(...)
 15. │             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 16. │               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 17. │                 └─value[[3L]](cond)
 18. │                   └─cli::cli_abort("File {full_url} could not be downloaded. {e}")
 19. │                     └─rlang::abort(...)
 20. │                       └─rlang:::signal_abort(cnd, .file)
 21. │                         └─base::signalCondition(cnd)
 22. ├─purrr (local) `<fn>`(`<rlng_rrr>`)
 23. │ └─cli::cli_abort(...)
 24. │   └─rlang::abort(...)
 25. │     └─rlang:::signal_abort(cnd, .file)
 26. │       └─base::signalCondition(cnd)
 27. └─base (local) `<fn>`(`<prrr_rr_>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
error in evaluating the argument '.data' in selecting a method for function 'join_features': ℹ In index: 1.
Caused by error in `value[[3L]]()`:
! File
  https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellxgene-0.2.1-hdf5/cpm/14583378cfb01c89f1a1fbb860f306dd/assays.h5
  could not be downloaded. Error in curl::curl_fetch_disk(url, x$path, handle =
  handle): Timeout was reached [object-store.rc.nectar.org.au]: Operation too
  slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted