Multiple platform build/check report for BioC 3.23 - BUILD results for annotate on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4961
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4690
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4627
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 annotate on kunpeng2

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

Version: 1.89.0

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

StartedAt: 2026-04-16 22:22:58 -0000 (Thu, 16 Apr 2026)

EndedAt: 2026-04-16 22:24:23 -0000 (Thu, 16 Apr 2026)

EllapsedTime: 85.1 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 annotate
###
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* checking for file ‘annotate/DESCRIPTION’ ... OK
* preparing ‘annotate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘chromLOC.Rmd’ using rmarkdown
--- finished re-building ‘chromLOC.Rmd’

--- re-building ‘useDataPkgs.Rmd’ using rmarkdown
--- finished re-building ‘useDataPkgs.Rmd’

--- re-building ‘GOusage.Rnw’ using Sweave

Attaching package: ‘graph’

The following object is masked from ‘package:XML’:

    addNode


Attaching package: ‘Rgraphviz’

The following object is masked from ‘package:annotate’:

    toFile

The following objects are masked from ‘package:IRanges’:

    from, to

The following objects are masked from ‘package:S4Vectors’:

    from, to

--- finished re-building ‘GOusage.Rnw’

--- re-building ‘annotate.Rnw’ using Sweave
--- finished re-building ‘annotate.Rnw’

--- re-building ‘prettyOutput.Rnw’ using Sweave
--- finished re-building ‘prettyOutput.Rnw’

--- re-building ‘query.Rnw’ using Sweave
Read 4 items
Read 3402 items
--- finished re-building ‘query.Rnw’

--- re-building ‘useProbeInfo.Rnw’ using Sweave
Loading required package: org.Rn.eg.db



Error: processing vignette 'useProbeInfo.Rnw' failed with diagnostics:
 chunk 3 (label = getACC) 
Error in file(con, "r") : 
  cannot open the connection to 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&id=NM_031013'

--- failed re-building ‘useProbeInfo.Rnw’

SUMMARY: processing the following file failed:
  ‘useProbeInfo.Rnw’

Error: Vignette re-building failed.
In addition: Warning message:
In file(con, "r") :
  cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&id=NM_031013': HTTP status was '502 Bad Gateway'
Execution halted