Multiple platform build/check report for BioC 3.22 - BUILD results for immunotation on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4596
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4538
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4535
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 immunotation on taishan

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

Version: 1.17.1

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

StartedAt: 2025-08-15 00:21:56 -0000 (Fri, 15 Aug 2025)

EndedAt: 2025-08-15 00:24:44 -0000 (Fri, 15 Aug 2025)

EllapsedTime: 168.1 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 immunotation
###
##############################################################################
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* checking for file ‘immunotation/DESCRIPTION’ ... OK
* preparing ‘immunotation’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘immunotation_vignette.Rmd’ using rmarkdown

Quitting from immunotation_vignette.Rmd:342-348 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `getURL()`:
! 'getURL()' failed:
  URL: http://www.allelefrequencies.net/hla6003a.asp?hla_locus1=A*02:01&hla_locus2=B*&hla_locus3=C*&hla_locus4=DRB1_not&hla_locus5=DPA1_not&hla_locus6=DPB1_not&hla_locus7=DQA1_not&hla_locus8=DQB1_not&hla_population=&hla_country=&hla_dataset=&hla_region=Europe&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_loci=
  error: cannot open the connection
---
Backtrace:
    ▆
 1. └─immunotation::query_haplotype_frequencies(...)
 2.   └─immunotation:::read_complete_freq_table(queryurl, type = "haplotype")
 3.     └─immunotation:::getURL(url, read_method = "html")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'immunotation_vignette.Rmd' failed with diagnostics:
'getURL()' failed:
  URL: http://www.allelefrequencies.net/hla6003a.asp?hla_locus1=A*02:01&hla_locus2=B*&hla_locus3=C*&hla_locus4=DRB1_not&hla_locus5=DPA1_not&hla_locus6=DPB1_not&hla_locus7=DQA1_not&hla_locus8=DQB1_not&hla_population=&hla_country=&hla_dataset=&hla_region=Europe&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_loci=
  error: cannot open the connection
--- failed re-building ‘immunotation_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted