Multiple platform build/check report for BioC 3.22 - BUILD results for cBioPortalData on kjohnson3

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"	4887
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4677
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4622
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4632
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 cBioPortalData on kjohnson3

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

raw results

Summary

Package: cBioPortalData

Version: 2.21.5

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cBioPortalData

StartedAt: 2025-10-17 15:51:11 -0400 (Fri, 17 Oct 2025)

EndedAt: 2025-10-17 15:52:08 -0400 (Fri, 17 Oct 2025)

EllapsedTime: 56.7 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cBioPortalData
###
##############################################################################
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* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* preparing ‘cBioPortalData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cBioPortalData.Rmd’ using rmarkdown
2025-10-17 15:52:03.425 R[40556:484715421] XType: Using static font registry.
--- finished re-building ‘cBioPortalData.Rmd’

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

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

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

Quitting from cgdsrMigration.Rmd:79-82 [sample_lists]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.invoke_fun()`:
! Not Found (HTTP 404).
---
Backtrace:
     ▆
  1. └─cBioPortalData::sampleLists(cbio, "gbm_tcga_pub")
  2.   └─cBioPortalData:::.invoke_bind(...)
  3.     ├─cBioPortalData:::.bind_content(.invoke_fun(api, name, ...))
  4.     │ ├─dplyr::bind_rows(httr::content(x))
  5.     │ │ └─rlang::list2(...)
  6.     │ └─httr::content(x)
  7.     │   ├─base::stopifnot(is.response(x))
  8.     │   └─httr:::is.response(x)
  9.     └─cBioPortalData:::.invoke_fun(api, name, ...)
 10.       └─httr::stop_for_status(res)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cgdsrMigration.Rmd' failed with diagnostics:
Not Found (HTTP 404).
--- failed re-building ‘cgdsrMigration.Rmd’

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

Error: Vignette re-building failed.
Execution halted