Multiple platform build/check report for BioC 3.22 - BUILD results for HPAanalyze 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"	4902
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 HPAanalyze on taishan

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

Version: 1.28.0

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

StartedAt: 2025-11-11 02:29:01 -0000 (Tue, 11 Nov 2025)

EndedAt: 2025-11-11 02:30:07 -0000 (Tue, 11 Nov 2025)

EllapsedTime: 66.0 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 HPAanalyze
###
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* checking for file ‘HPAanalyze/DESCRIPTION’ ... OK
* preparing ‘HPAanalyze’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘a_HPAanalyze_quick_start.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is ""1. Quick-start guide: Acquire and visualize the Human Protein Atlas (HPA) data in one function with HPAanalyze"", and the latter is "1. Quick-start guide: Acquire and visualize the Human Protein Atlas (HPA) data in one function with HPAanalyze". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘a_HPAanalyze_quick_start.Rmd’

--- re-building ‘b_HPAanalyze_indepth.Rmd’ using rmarkdown
trying URL 'https://v23.proteinatlas.org/download/normal_tissue.tsv.zip'
Content type 'application/zip' length 5615221 bytes (5.4 MB)
================================================
downloaded 5.2 MB


Quitting from b_HPAanalyze_indepth.Rmd:174-177 [subset1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! download from 'https://v23.proteinatlas.org/download/normal_tissue.tsv.zip' failed
---
Backtrace:
    ▆
 1. └─HPAanalyze::hpaDownload(downloadList = "histology", version = "v23")
 2.   └─utils::download.file(url = downloadDatasets$link[[i]], destfile = temp)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'b_HPAanalyze_indepth.Rmd' failed with diagnostics:
download from 'https://v23.proteinatlas.org/download/normal_tissue.tsv.zip' failed
--- failed re-building ‘b_HPAanalyze_indepth.Rmd’

--- re-building ‘c_HPAanalyze_case_query.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is ""3. Tutorial: Combine HPAanalyze with your Human Protein Atlas (HPA) queries"", and the latter is "3. Tutorial: Combine HPAanalyze with your Human Protein Atlas (HPA) queries". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘c_HPAanalyze_case_query.Rmd’

--- re-building ‘d_HPAanalyze_case_offline_xml.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is ""4. Tutorial: Working with Human Protein Atlas (HPA) xml files offline"", and the latter is "4. Tutorial: Working with Human Protein Atlas (HPA) xml files offline". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘d_HPAanalyze_case_offline_xml.Rmd’

--- re-building ‘e_HPAanalyze_case_json.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is ""5. Tutorial: Export Human Protein Atlas (HPA) data as JSON"", and the latter is "5. Tutorial: Export Human Protein Atlas (HPA) data as JSON". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘e_HPAanalyze_case_json.Rmd’

--- re-building ‘f_HPAanalyze_case_images.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is ""6. Tutorial: Download histology images from the Human Protein Atlas"", and the latter is "6. Tutorial: Download histology images from the Human Protein Atlas". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘f_HPAanalyze_case_images.Rmd’

--- re-building ‘z_HPAanalyze_paper_figures.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is ""99. Code for figures from HPAanalyze paper"", and the latter is "99. Code for figures from HPAanalyze paper". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘z_HPAanalyze_paper_figures.Rmd’

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

Error: Vignette re-building failed.
Execution halted