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This page was generated on 2025-02-06 12:12 -0500 (Thu, 06 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4753
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4501
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4524
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4476
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4407
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 2123/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAbiolinks 2.34.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 2025)
git_url: https://git.bioconductor.org/packages/TCGAbiolinks
git_branch: RELEASE_3_20
git_last_commit: 32384fa
git_last_commit_date: 2024-10-29 10:03:07 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

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: 2.34.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAbiolinks
StartedAt: 2025-02-04 03:28:55 -0000 (Tue, 04 Feb 2025)
EndedAt: 2025-02-04 03:36:23 -0000 (Tue, 04 Feb 2025)
EllapsedTime: 448.7 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 2025-02-04 03:33:37.0340884 is 38.85320662 s in the future
/usr/bin/gtar: 2c9512eb-e075-4e45-8ad4-b00048a6d47e/nationwidechildrens.org_clinical_nte_acc.txt: time stamp 2025-02-04 03:33:37.034846 is 38.85380848 s in the future
/usr/bin/gtar: 4612e74a-f374-459a-a14f-8cecdb1c14f8/nationwidechildrens.org_clinical_radiation_acc.txt: time stamp 2025-02-04 03:33:37.0355673 is 38.85444892 s in the future
/usr/bin/gtar: 490dfbb2-42e0-41da-8c04-a6f307b27e5c/nationwidechildrens.org_clinical_follow_up_v4.0_nte_acc.txt: time stamp 2025-02-04 03:33:37.036093 is 38.85490358 s in the future
/usr/bin/gtar: 4c259f88-b551-4e17-b78f-4c1249b288da/nationwidechildrens.org_clinical_drug_acc.txt: time stamp 2025-02-04 03:33:37.036639 is 38.85538006 s in the future
/usr/bin/gtar: 6a22c17f-3963-4a6f-a03d-d4fd3fd6309e/nationwidechildrens.org_clinical_follow_up_v4.0_acc.txt: time stamp 2025-02-04 03:33:37.0372055 is 38.84839006 s in the future
/usr/bin/gtar: 88e04b32-4f73-4b6d-aa96-be6769d6ea59/nationwidechildrens.org_clinical_omf_v4.0_acc.txt: time stamp 2025-02-04 03:33:37.0387328 is 38.84977334 s in the future
/usr/bin/gtar: 909f0719-b165-4beb-9fb3-f21aff071469/nationwidechildrens.org_clinical_patient_acc.txt: time stamp 2025-02-04 03:33:37.0392725 is 38.84643084 s in the future
/usr/bin/gtar: MANIFEST.txt: time stamp 2025-02-04 03:34:20.6699939 is 38.3610349 s in the future
/usr/bin/gtar: 041c5d01-3156-4803-840d-f196e8a77155/nationwidechildrens.org_ssf_tumor_samples_acc.txt: time stamp 2025-02-04 03:34:20.670247 is 38.36111833 s in the future
/usr/bin/gtar: 05b8efda-aa93-4c04-8beb-ffc95c062af9/nationwidechildrens.org_biospecimen_portion_acc.txt: time stamp 2025-02-04 03:34:20.671866 is 38.35905205 s in the future
/usr/bin/gtar: 3584d028-b901-4c5b-98c9-4dd120b3836f/nationwidechildrens.org_biospecimen_slide_acc.txt: time stamp 2025-02-04 03:34:20.676666 is 38.36373866 s in the future
/usr/bin/gtar: 52a113be-a3d8-40ea-bebe-93e62d91ade6/nationwidechildrens.org_ssf_normal_controls_acc.txt: time stamp 2025-02-04 03:34:20.677828 is 38.36481851 s in the future
/usr/bin/gtar: 59a34fdf-f372-4694-bc45-47f412049425/nationwidechildrens.org_biospecimen_protocol_acc.txt: time stamp 2025-02-04 03:34:20.678828 is 38.3619979 s in the future
/usr/bin/gtar: 59e14613-6a21-43be-8f0f-15f23e71f3c6/nationwidechildrens.org_biospecimen_analyte_acc.txt: time stamp 2025-02-04 03:34:20.6805089 is 38.35168896 s in the future
/usr/bin/gtar: 84f52527-e0e2-447c-a905-3616c41a7e9d/nationwidechildrens.org_biospecimen_aliquot_acc.txt: time stamp 2025-02-04 03:34:20.6953056 is 38.35453081 s in the future
/usr/bin/gtar: 9ad06cec-a27f-4093-8773-b857ef200f4b/nationwidechildrens.org_biospecimen_diagnostic_slides_acc.txt: time stamp 2025-02-04 03:34:20.716053 is 38.37515627 s in the future
/usr/bin/gtar: d03cb5ec-7e3f-450f-9a8e-380bd9e52d10/nationwidechildrens.org_biospecimen_sample_acc.txt: time stamp 2025-02-04 03:34:20.7179613 is 38.37692734 s in the future
/usr/bin/gtar: d86d9ee4-5394-4d9a-8d4b-9b219a2e2ea8/nationwidechildrens.org_biospecimen_shipment_portion_acc.txt: time stamp 2025-02-04 03:34:20.7219718 is 38.380864 s in the future

Quitting from lines 139-140 [unnamed-chunk-7] (clinical.Rmd)
Error: processing vignette 'clinical.Rmd' failed with diagnostics:
Supplied 92 items to be assigned to 170 items of column 'submitter_id'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code.
--- 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

Quitting from lines 313-320 [unnamed-chunk-9] (query.Rmd)
Error: processing vignette 'query.Rmd' failed with diagnostics:
cannot open the connection
--- failed 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 files failed:
  ‘clinical.Rmd’ ‘query.Rmd’

Error: Vignette re-building failed.
Execution halted