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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4883
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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 TCGAbiolinks on taishan

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

Version: 2.38.0

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

StartedAt: 2025-12-30 06:07:49 -0000 (Tue, 30 Dec 2025)

EndedAt: 2025-12-30 06:20:36 -0000 (Tue, 30 Dec 2025)

EllapsedTime: 766.4 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 TCGAbiolinks
###
##############################################################################
##############################################################################


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

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

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

--- re-building ‘clinical.Rmd’ using rmarkdown
/usr/bin/gtar: MANIFEST.txt: time stamp 2025-12-30 06:17:31.016289 is 359.01636666 s in the future
/usr/bin/gtar: 2c9512eb-e075-4e45-8ad4-b00048a6d47e/nationwidechildrens.org_clinical_nte_acc.txt: time stamp 2025-12-30 06:17:31.0175354 is 359.01744388 s in the future
/usr/bin/gtar: 4612e74a-f374-459a-a14f-8cecdb1c14f8/nationwidechildrens.org_clinical_radiation_acc.txt: time stamp 2025-12-30 06:17:31.0191119 is 359.01893317 s in the future
/usr/bin/gtar: 490dfbb2-42e0-41da-8c04-a6f307b27e5c/nationwidechildrens.org_clinical_follow_up_v4.0_nte_acc.txt: time stamp 2025-12-30 06:17:31.0203612 is 359.02010613 s in the future
/usr/bin/gtar: 4c259f88-b551-4e17-b78f-4c1249b288da/nationwidechildrens.org_clinical_drug_acc.txt: time stamp 2025-12-30 06:17:31.0214477 is 359.02111919 s in the future
/usr/bin/gtar: 6a22c17f-3963-4a6f-a03d-d4fd3fd6309e/nationwidechildrens.org_clinical_follow_up_v4.0_acc.txt: time stamp 2025-12-30 06:17:31.0227554 is 359.02223297 s in the future
/usr/bin/gtar: 88e04b32-4f73-4b6d-aa96-be6769d6ea59/nationwidechildrens.org_clinical_omf_v4.0_acc.txt: time stamp 2025-12-30 06:17:31.0249572 is 359.02436315 s in the future
/usr/bin/gtar: 909f0719-b165-4beb-9fb3-f21aff071469/nationwidechildrens.org_clinical_patient_acc.txt: time stamp 2025-12-30 06:17:31.026053 is 359.02480518 s in the future
/usr/bin/gtar: MANIFEST.txt: time stamp 2025-12-30 06:18:43.1134813 is 358.47582936 s in the future
/usr/bin/gtar: 041c5d01-3156-4803-840d-f196e8a77155/nationwidechildrens.org_ssf_tumor_samples_acc.txt: time stamp 2025-12-30 06:18:43.1140482 is 358.47619699 s in the future
/usr/bin/gtar: 05b8efda-aa93-4c04-8beb-ffc95c062af9/nationwidechildrens.org_biospecimen_portion_acc.txt: time stamp 2025-12-30 06:18:43.1190338 is 358.4810542 s in the future
/usr/bin/gtar: 3584d028-b901-4c5b-98c9-4dd120b3836f/nationwidechildrens.org_biospecimen_slide_acc.txt: time stamp 2025-12-30 06:18:43.125199 is 358.48710358 s in the future
/usr/bin/gtar: 52a113be-a3d8-40ea-bebe-93e62d91ade6/nationwidechildrens.org_ssf_normal_controls_acc.txt: time stamp 2025-12-30 06:18:43.13098 is 358.49278157 s in the future
/usr/bin/gtar: 59a34fdf-f372-4694-bc45-47f412049425/nationwidechildrens.org_biospecimen_protocol_acc.txt: time stamp 2025-12-30 06:18:43.1337566 is 358.49538755 s in the future
/usr/bin/gtar: 59e14613-6a21-43be-8f0f-15f23e71f3c6/nationwidechildrens.org_biospecimen_analyte_acc.txt: time stamp 2025-12-30 06:18:43.1432424 is 358.50450839 s in the future
/usr/bin/gtar: 84f52527-e0e2-447c-a905-3616c41a7e9d/nationwidechildrens.org_biospecimen_aliquot_acc.txt: time stamp 2025-12-30 06:18:43.1627786 is 358.52347845 s in the future
/usr/bin/gtar: 9ad06cec-a27f-4093-8773-b857ef200f4b/nationwidechildrens.org_biospecimen_diagnostic_slides_acc.txt: time stamp 2025-12-30 06:18:43.179211 is 358.53976758 s in the future
/usr/bin/gtar: d03cb5ec-7e3f-450f-9a8e-380bd9e52d10/nationwidechildrens.org_biospecimen_sample_acc.txt: time stamp 2025-12-30 06:18:43.191779 is 358.55204865 s in the future
/usr/bin/gtar: d86d9ee4-5394-4d9a-8d4b-9b219a2e2ea8/nationwidechildrens.org_biospecimen_shipment_portion_acc.txt: time stamp 2025-12-30 06:18:43.1978796 is 358.55803289 s in the future
/usr/bin/gtar: MANIFEST.txt: time stamp 2025-12-30 06:20:11.417299 is 359.28204267 s in the future
/usr/bin/gtar: 2180bc9c-51c9-4725-a6c7-6b7436aae439/nationwidechildrens.org_clinical.TCGA-RU-A8FL.xml: time stamp 2025-12-30 06:20:11.4186387 is 359.28315186 s in the future
/usr/bin/gtar: 726fbbb5-bd0f-452e-9fbb-691002066fac/nationwidechildrens.org_clinical.TCGA-AA-3972.xml: time stamp 2025-12-30 06:20:11.4212582 is 359.28562205 s in the future

Quitting from clinical.Rmd:262-271 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://api.gdc.cancer.gov/projects/TCGA-COAD?expand=summary,summary.data_categories&pretty=true'
---
Backtrace:
    ▆
 1. └─TCGAbiolinks::GDCquery(...)
 2.   └─TCGAbiolinks:::checkDataCategoriesInput(project, data.category) at TCGAbiolinks/R/query.R:216:5
 3.     └─TCGAbiolinks::getProjectSummary(proj) at TCGAbiolinks/R/internal.R:110:9
 4.       └─jsonlite::fromJSON(url, simplifyDataFrame = TRUE) at TCGAbiolinks/R/api.R:291:5
 5.         └─jsonlite:::parse_and_simplify(...)
 6.           └─jsonlite:::parseJSON(txt, bigint_as_char)
 7.             └─jsonlite:::parse_con(txt, bigint_as_char)
 8.               ├─base::open(con, "rb")
 9.               └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clinical.Rmd' failed with diagnostics:
cannot open the connection to 'https://api.gdc.cancer.gov/projects/TCGA-COAD?expand=summary,summary.data_categories&pretty=true'
--- failed re-building ‘clinical.Rmd’

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

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted