Multiple platform build/check report for BioC 3.22 - BUILD results for gDNAx on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4810
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4528
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4493
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 gDNAx on nebbiolo2

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

raw results

Summary

Package: gDNAx

Version: 1.7.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gDNAx

StartedAt: 2025-06-18 17:36:08 -0400 (Wed, 18 Jun 2025)

EndedAt: 2025-06-18 17:37:25 -0400 (Wed, 18 Jun 2025)

EllapsedTime: 77.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gDNAx
###
##############################################################################
##############################################################################


* checking for file ‘gDNAx/DESCRIPTION’ ... OK
* preparing ‘gDNAx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gDNAx.Rmd’ using rmarkdown
[E::hts_hopen] Failed to open file /tmp/RtmpscE9k1/s27gDNA1.bam
[E::hts_open_format] Failed to open file "/tmp/RtmpscE9k1/s27gDNA1.bam" : Exec format error

Quitting from gDNAx.Rmd:100-106 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'obj' in selecting a method for function 'unname': isOpen(<BamFile>) is not 'TRUE'
---
Backtrace:
     ▆
  1. ├─gDNAx::gDNAdx(bamfiles, txdb)
  2. │ └─gDNAx:::.checkPairedEnd(bfl, singleEnd, BPPARAM)
  3. │   ├─S4Vectors::unname(vapply(bfl, testpe, FUN.VALUE = logical(1L)))
  4. │   └─base::vapply(bfl, testpe, FUN.VALUE = logical(1L))
  5. │     └─gDNAx (local) FUN(X[[i]], ...)
  6. │       ├─base::close(bf)
  7. │       └─Rsamtools::close.BamFile(bf)
  8. │         └─base::stop("isOpen(<BamFile>) is not 'TRUE'")
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gDNAx.Rmd' failed with diagnostics:
error in evaluating the argument 'obj' in selecting a method for function 'unname': isOpen(<BamFile>) is not 'TRUE'
--- failed re-building ‘gDNAx.Rmd’

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

Error: Vignette re-building failed.
Execution halted