Multiple platform build/check report for BioC 3.22 - BUILD results for SNPediaR 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"	4827
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4614
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4558
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4560
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 SNPediaR on taishan

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

Version: 1.35.0

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

StartedAt: 2025-09-23 03:20:36 -0000 (Tue, 23 Sep 2025)

EndedAt: 2025-09-23 03:20:58 -0000 (Tue, 23 Sep 2025)

EllapsedTime: 22.0 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 SNPediaR
###
##############################################################################
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* checking for file ‘SNPediaR/DESCRIPTION’ ... OK
* preparing ‘SNPediaR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SNPediaR.Rmd’ using rmarkdown

Quitting from SNPediaR.Rmd:116-120 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^
---
Backtrace:
    ▆
 1. └─SNPediaR::getPages(titles = c("Rs53576", "Rs1815739"), wikiParseFunction = findPMID)
 2.   └─jsonlite::fromJSON(datos)
 3.     └─jsonlite:::parse_and_simplify(...)
 4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
 5.         └─jsonlite:::parse_string(txt, bigint_as_char)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SNPediaR.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                       <html> \n<head><title>502 Bad G
                     (right here) ------^

--- failed re-building ‘SNPediaR.Rmd’

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

Error: Vignette re-building failed.
Execution halted