Tiago Chedraoui Silva
| Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/TCGAbiolinks |
| git_branch: devel |
| git_last_commit: 2072af1 |
| git_last_commit_date: 2025-10-29 10:27:16 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:38 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 2232/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.39.0 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for TCGAbiolinks in R Universe. | ||||||||||||||
|
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. |
| Package: TCGAbiolinks |
| Version: 2.39.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks |
| StartedAt: 2026-04-17 02:13:17 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 02:24:01 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 643.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks
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* 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 2026-04-17 02:17:16.8518603 is 7.01400357 s in the future
/usr/bin/gtar: 6a22c17f-3963-4a6f-a03d-d4fd3fd6309e/nationwidechildrens.org_clinical_follow_up_v4.0_acc.txt: time stamp 2026-04-17 02:17:16.8522704 is 7.0142352 s in the future
/usr/bin/gtar: 909f0719-b165-4beb-9fb3-f21aff071469/nationwidechildrens.org_clinical_patient_acc.txt: time stamp 2026-04-17 02:17:16.8534865 is 7.01518347 s in the future
/usr/bin/gtar: 88e04b32-4f73-4b6d-aa96-be6769d6ea59/nationwidechildrens.org_clinical_omf_v4.0_acc.txt: time stamp 2026-04-17 02:17:16.8580241 is 7.01963281 s in the future
/usr/bin/gtar: 490dfbb2-42e0-41da-8c04-a6f307b27e5c/nationwidechildrens.org_clinical_follow_up_v4.0_nte_acc.txt: time stamp 2026-04-17 02:17:16.858623 is 7.02016325 s in the future
/usr/bin/gtar: 2c9512eb-e075-4e45-8ad4-b00048a6d47e/nationwidechildrens.org_clinical_nte_acc.txt: time stamp 2026-04-17 02:17:16.8590727 is 7.02053701 s in the future
/usr/bin/gtar: 4612e74a-f374-459a-a14f-8cecdb1c14f8/nationwidechildrens.org_clinical_radiation_acc.txt: time stamp 2026-04-17 02:17:16.8597498 is 7.02114706 s in the future
/usr/bin/gtar: 4c259f88-b551-4e17-b78f-4c1249b288da/nationwidechildrens.org_clinical_drug_acc.txt: time stamp 2026-04-17 02:17:16.8604555 is 7.02178398 s in the future
/usr/bin/gtar: MANIFEST.txt: time stamp 2026-04-17 02:18:20.7505574 is 6.51077763 s in the future
/usr/bin/gtar: d86d9ee4-5394-4d9a-8d4b-9b219a2e2ea8/nationwidechildrens.org_biospecimen_shipment_portion_acc.txt: time stamp 2026-04-17 02:18:20.7510176 is 6.5110792 s in the future
/usr/bin/gtar: 9ad06cec-a27f-4093-8773-b857ef200f4b/nationwidechildrens.org_biospecimen_diagnostic_slides_acc.txt: time stamp 2026-04-17 02:18:20.7516985 is 6.51165053 s in the future
/usr/bin/gtar: 52a113be-a3d8-40ea-bebe-93e62d91ade6/nationwidechildrens.org_ssf_normal_controls_acc.txt: time stamp 2026-04-17 02:18:20.7527535 is 6.51261535 s in the future
/usr/bin/gtar: 041c5d01-3156-4803-840d-f196e8a77155/nationwidechildrens.org_ssf_tumor_samples_acc.txt: time stamp 2026-04-17 02:18:20.7536106 is 6.51337745 s in the future
/usr/bin/gtar: 59a34fdf-f372-4694-bc45-47f412049425/nationwidechildrens.org_biospecimen_protocol_acc.txt: time stamp 2026-04-17 02:18:20.7546513 is 6.5142981 s in the future
/usr/bin/gtar: 05b8efda-aa93-4c04-8beb-ffc95c062af9/nationwidechildrens.org_biospecimen_portion_acc.txt: time stamp 2026-04-17 02:18:20.7567756 is 6.5162944 s in the future
/usr/bin/gtar: 3584d028-b901-4c5b-98c9-4dd120b3836f/nationwidechildrens.org_biospecimen_slide_acc.txt: time stamp 2026-04-17 02:18:20.759621 is 6.51902207 s in the future
/usr/bin/gtar: 84f52527-e0e2-447c-a905-3616c41a7e9d/nationwidechildrens.org_biospecimen_aliquot_acc.txt: time stamp 2026-04-17 02:18:20.7607694 is 6.5196613 s in the future
/usr/bin/gtar: 59e14613-6a21-43be-8f0f-15f23e71f3c6/nationwidechildrens.org_biospecimen_analyte_acc.txt: time stamp 2026-04-17 02:18:20.7760305 is 6.53459928 s in the future
/usr/bin/gtar: d03cb5ec-7e3f-450f-9a8e-380bd9e52d10/nationwidechildrens.org_biospecimen_sample_acc.txt: time stamp 2026-04-17 02:18:20.7905989 is 6.54899951 s in the future
/usr/bin/gtar: MANIFEST.txt: time stamp 2026-04-17 02:19:35.378293 is 7.22462026 s in the future
/usr/bin/gtar: 726fbbb5-bd0f-452e-9fbb-691002066fac/nationwidechildrens.org_clinical.TCGA-AA-3972.xml: time stamp 2026-04-17 02:19:35.3796113 is 7.22570526 s in the future
/usr/bin/gtar: 2180bc9c-51c9-4725-a6c7-6b7436aae439/nationwidechildrens.org_clinical.TCGA-RU-A8FL.xml: time stamp 2026-04-17 02:19:35.3834856 is 7.22943691 s in the future
--- finished 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
Quitting from stemness_score.Rmd:51-83 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! EDASeq package is needed for this function to work. Please install it.
---
Backtrace:
▆
1. └─TCGAbiolinks::TCGAanalyze_Normalization(tabDF = dataBRCA, geneInfo = geneInfo)
2. └─TCGAbiolinks:::check_package("EDASeq") at TCGAbiolinks/R/analyze.R:585:5
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'stemness_score.Rmd' failed with diagnostics:
EDASeq package is needed for this function to work. Please install it.
--- failed re-building ‘stemness_score.Rmd’
--- re-building ‘subtypes.Rmd’ using rmarkdown
--- finished re-building ‘subtypes.Rmd’
SUMMARY: processing the following file failed:
‘stemness_score.Rmd’
Error: Vignette re-building failed.
Execution halted