Multiple platform build/check report for BioC 3.22 - BUILD results for SpatialDecon 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"	4814
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4603
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4547
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4553
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 SpatialDecon on taishan

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

Version: 1.19.0

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

StartedAt: 2025-09-19 04:12:27 -0000 (Fri, 19 Sep 2025)

EndedAt: 2025-09-19 04:13:19 -0000 (Fri, 19 Sep 2025)

EllapsedTime: 52.0 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 SpatialDecon
###
##############################################################################
##############################################################################


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

Quitting from SpatialDecon_vignette.Rmd:139-154 [downloadmatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://raw.github.com/Nanostring-Biostats/CellProfileLibrary/master/Mouse/Mouse_datasets_metadata.csv'
---
Backtrace:
    ▆
 1. └─SpatialDecon::download_profile_matrix(...)
 2.   └─utils::read.csv(...)
 3.     └─utils::read.table(...)
 4.       └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SpatialDecon_vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.github.com/Nanostring-Biostats/CellProfileLibrary/master/Mouse/Mouse_datasets_metadata.csv'
--- failed re-building ‘SpatialDecon_vignette.Rmd’

--- re-building ‘SpatialDecon_vignette_NSCLC.Rmd’ using rmarkdown

Quitting from SpatialDecon_vignette_NSCLC.Rmd:132-147 [downloadmatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download_data_intern()`:
! Service Unavailable (HTTP 503).
---
Backtrace:
    ▆
 1. └─SpatialDecon::download_profile_matrix(...)
 2.   ├─base::suppressMessages(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   └─repmis::source_data(...)
 5.     └─repmis:::download_data_intern(url = url, sha1 = sha1, temp_file = temp_file)
 6.       └─httr::stop_for_status(request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SpatialDecon_vignette_NSCLC.Rmd' failed with diagnostics:
Service Unavailable (HTTP 503).
--- failed re-building ‘SpatialDecon_vignette_NSCLC.Rmd’

SUMMARY: processing the following files failed:
  ‘SpatialDecon_vignette.Rmd’ ‘SpatialDecon_vignette_NSCLC.Rmd’

Error: Vignette re-building failed.
Execution halted