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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 2025-01-31 03:12:39.8892908 is 34.74004861 s in the future
/usr/bin/gtar: 2c9512eb-e075-4e45-8ad4-b00048a6d47e/nationwidechildrens.org_clinical_nte_acc.txt: time stamp 2025-01-31 03:12:39.8897583 is 34.74036263 s in the future
/usr/bin/gtar: 4612e74a-f374-459a-a14f-8cecdb1c14f8/nationwidechildrens.org_clinical_radiation_acc.txt: time stamp 2025-01-31 03:12:39.8907254 is 34.74124953 s in the future
/usr/bin/gtar: 490dfbb2-42e0-41da-8c04-a6f307b27e5c/nationwidechildrens.org_clinical_follow_up_v4.0_nte_acc.txt: time stamp 2025-01-31 03:12:39.8914137 is 34.74187003 s in the future
/usr/bin/gtar: 4c259f88-b551-4e17-b78f-4c1249b288da/nationwidechildrens.org_clinical_drug_acc.txt: time stamp 2025-01-31 03:12:39.8919759 is 34.74236064 s in the future
/usr/bin/gtar: 6a22c17f-3963-4a6f-a03d-d4fd3fd6309e/nationwidechildrens.org_clinical_follow_up_v4.0_acc.txt: time stamp 2025-01-31 03:12:39.8927028 is 34.74290667 s in the future
/usr/bin/gtar: 88e04b32-4f73-4b6d-aa96-be6769d6ea59/nationwidechildrens.org_clinical_omf_v4.0_acc.txt: time stamp 2025-01-31 03:12:39.893704 is 34.74383861 s in the future
/usr/bin/gtar: 909f0719-b165-4beb-9fb3-f21aff071469/nationwidechildrens.org_clinical_patient_acc.txt: time stamp 2025-01-31 03:12:39.8941789 is 34.74395601 s in the future
/usr/bin/gtar: MANIFEST.txt: time stamp 2025-01-31 03:13:23.5278196 is 34.08576954 s in the future
/usr/bin/gtar: 041c5d01-3156-4803-840d-f196e8a77155/nationwidechildrens.org_ssf_tumor_samples_acc.txt: time stamp 2025-01-31 03:13:23.5282402 is 34.08600272 s in the future
/usr/bin/gtar: 05b8efda-aa93-4c04-8beb-ffc95c062af9/nationwidechildrens.org_biospecimen_portion_acc.txt: time stamp 2025-01-31 03:13:23.529622 is 34.08713562 s in the future
/usr/bin/gtar: 3584d028-b901-4c5b-98c9-4dd120b3836f/nationwidechildrens.org_biospecimen_slide_acc.txt: time stamp 2025-01-31 03:13:23.531913 is 34.08932791 s in the future
/usr/bin/gtar: 52a113be-a3d8-40ea-bebe-93e62d91ade6/nationwidechildrens.org_ssf_normal_controls_acc.txt: time stamp 2025-01-31 03:13:23.5333087 is 34.09063824 s in the future
/usr/bin/gtar: 59a34fdf-f372-4694-bc45-47f412049425/nationwidechildrens.org_biospecimen_protocol_acc.txt: time stamp 2025-01-31 03:13:23.5349877 is 34.09202669 s in the future
/usr/bin/gtar: 59e14613-6a21-43be-8f0f-15f23e71f3c6/nationwidechildrens.org_biospecimen_analyte_acc.txt: time stamp 2025-01-31 03:13:23.537183 is 34.09360226 s in the future
/usr/bin/gtar: 84f52527-e0e2-447c-a905-3616c41a7e9d/nationwidechildrens.org_biospecimen_aliquot_acc.txt: time stamp 2025-01-31 03:13:23.5426924 is 34.09841739 s in the future
/usr/bin/gtar: 9ad06cec-a27f-4093-8773-b857ef200f4b/nationwidechildrens.org_biospecimen_diagnostic_slides_acc.txt: time stamp 2025-01-31 03:13:23.5526395 is 34.1080718 s in the future
/usr/bin/gtar: d03cb5ec-7e3f-450f-9a8e-380bd9e52d10/nationwidechildrens.org_biospecimen_sample_acc.txt: time stamp 2025-01-31 03:13:23.554586 is 34.10967723 s in the future
/usr/bin/gtar: d86d9ee4-5394-4d9a-8d4b-9b219a2e2ea8/nationwidechildrens.org_biospecimen_shipment_portion_acc.txt: time stamp 2025-01-31 03:13:23.5593777 is 34.11437253 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