| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-04 11:35 -0400 (Mon, 04 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4989 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4719 |
| 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 | ||||
| Package 298/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cBioPortalData 2.24.0 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for cBioPortalData in R Universe. | ||||||||||||||
|
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. |
| Package: cBioPortalData |
| Version: 2.24.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cBioPortalData |
| StartedAt: 2026-05-03 16:44:28 -0400 (Sun, 03 May 2026) |
| EndedAt: 2026-05-03 16:46:16 -0400 (Sun, 03 May 2026) |
| EllapsedTime: 108.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘cBioPortalData.Rmd’ using rmarkdown
Quitting from cBioPortalData.Rmd:137-149 [cbioportaldata]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `httr::content(res)[["message"]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─cBioPortalData::cBioPortalData(...)
2. └─cBioPortalData:::.portalExperiments(...)
3. └─cBioPortalData::getDataByGenes(...)
4. └─cBioPortalData::allSamples(api, studyId)
5. └─cBioPortalData:::.invoke_bind(...)
6. ├─cBioPortalData:::.bind_content(.invoke_fun(api, name, ...))
7. │ ├─dplyr::bind_rows(httr::content(x))
8. │ │ └─rlang::list2(...)
9. │ └─httr::content(x)
10. │ ├─base::stopifnot(is.response(x))
11. │ └─httr:::is.response(x)
12. └─cBioPortalData:::.invoke_fun(api, name, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cBioPortalData.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘cBioPortalData.Rmd’
--- re-building ‘cBioPortalDataErrors.Rmd’ using rmarkdown
--- finished re-building ‘cBioPortalDataErrors.Rmd’
--- re-building ‘cBioPortalRClient.Rmd’ using rmarkdown
Quitting from cBioPortalRClient.Rmd:73-75 [cbioportal_client]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! '.service_get_api_file' failed:
Service Unavailable (HTTP 503).
---
Backtrace:
▆
1. └─cBioPortalData::cBioPortal()
2. ├─base::withCallingHandlers(...)
3. └─AnVIL::Service(...)
4. └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
5. └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cBioPortalRClient.Rmd' failed with diagnostics:
'.service_get_api_file' failed:
Service Unavailable (HTTP 503).
--- failed re-building ‘cBioPortalRClient.Rmd’
--- re-building ‘cgdsrMigration.Rmd’ using rmarkdown
Quitting from cgdsrMigration.Rmd:41-48 [cbioportal_setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! '.service_get_api_file' failed:
Service Unavailable (HTTP 503).
---
Backtrace:
▆
1. └─cBioPortalData::cBioPortal(...)
2. ├─base::withCallingHandlers(...)
3. └─AnVIL::Service(...)
4. └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
5. └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cgdsrMigration.Rmd' failed with diagnostics:
'.service_get_api_file' failed:
Service Unavailable (HTTP 503).
--- failed re-building ‘cgdsrMigration.Rmd’
SUMMARY: processing the following files failed:
‘cBioPortalData.Rmd’ ‘cBioPortalRClient.Rmd’ ‘cgdsrMigration.Rmd’
Error: Vignette re-building failed.
Execution halted