Multiple platform build/check report for BioC 3.22 - BUILD results for raer 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"	4903
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 raer on taishan

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

Version: 1.8.0

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

StartedAt: 2025-11-14 04:25:05 -0000 (Fri, 14 Nov 2025)

EndedAt: 2025-11-14 04:27:13 -0000 (Fri, 14 Nov 2025)

EllapsedTime: 128.1 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 raer
###
##############################################################################
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* checking for file ‘raer/DESCRIPTION’ ... OK
* preparing ‘raer’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘raer.Rmd’ using rmarkdown
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read_block] Failed to read BGZF block data at offset 113796956 expected 8808 bytes; hread returned 2194
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
[raer internal] error detected during pileup, -1

Quitting from raer.Rmd:152-172 [pileup_cells]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! BiocParallel errors
  1 remote errors, element index: 8
  17 unevaluated and other errors
  first remote error:
Error in (function (bamfn, index, id, sites, barcodes, outfile_prefix, : pileup failed
---
Backtrace:
    ▆
 1. └─raer::pileup_cells(...)
 2.   ├─BiocParallel::bpmapply(...)
 3.   └─BiocParallel::bpmapply(...)
 4.     ├─BiocParallel::bplapply(...)
 5.     └─BiocParallel::bplapply(...)
 6.       └─BiocParallel:::.bpinit(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'raer.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 8
  17 unevaluated and other errors
  first remote error:
Error in (function (bamfn, index, id, sites, barcodes, outfile_prefix, : pileup failed

--- failed re-building ‘raer.Rmd’

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

Error: Vignette re-building failed.
Execution halted