Build/check report for BioC 3.22 experimental data - BUILD results for gDNAinRNAseqData on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4786
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 gDNAinRNAseqData on nebbiolo2

To the developers/maintainers of the gDNAinRNAseqData package:
- 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: gDNAinRNAseqData

Version: 1.10.0

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

StartedAt: 2025-11-18 11:31:18 -0500 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 11:31:51 -0500 (Tue, 18 Nov 2025)

EllapsedTime: 32.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gDNAinRNAseqData
###
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* checking for file ‘gDNAinRNAseqData/DESCRIPTION’ ... OK
* preparing ‘gDNAinRNAseqData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gDNAinRNAseqData.Rmd’ using rmarkdown

Quitting from gDNAinRNAseqData.Rmd:60-65 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: EH8079
  title: RNA-seq data BAM file subset of HRR589632 contaminated with 0% gDNA
  reason: 2 resources failed to download
---
Backtrace:
     ▆
  1. └─gDNAinRNAseqData::LiYu22subsetBAMfiles()
  2.   ├─ehres[[i]]
  3.   └─ehres[[i]]
  4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
  5.       ├─methods::callNextMethod(...)
  6.       │ └─base::eval(call, callEnv)
  7.       │   └─base::eval(call, callEnv)
  8.       └─AnnotationHub (local) .nextMethod(...)
  9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 10.           └─AnnotationHub:::.Hub_get1(...)
 11.             └─base::tryCatch(...)
 12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                   └─value[[3L]](cond)
 15.                     └─base::tryCatch(...)
 16.                       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 17.                         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 18.                           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gDNAinRNAseqData.Rmd' failed with diagnostics:
failed to load resource
  name: EH8079
  title: RNA-seq data BAM file subset of HRR589632 contaminated with 0% gDNA
  reason: 2 resources failed to download
--- failed re-building ‘gDNAinRNAseqData.Rmd’

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

Error: Vignette re-building failed.
Execution halted