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### Running command:
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###   chmod a+r TCGAutils -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TCGAutils
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* checking for file 'TCGAutils/DESCRIPTION' ... OK
* preparing 'TCGAutils':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'TCGAutils.Rmd' using rmarkdown
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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    as.data.frame, basename, cbind, colnames, dirname, do.call,
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    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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Loading required package: IRanges

Attaching package: 'IRanges'

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Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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Attaching package: 'MultiAssayExperiment'

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    splitAssays


Attaching package: 'RTCGAToolbox'

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    makeSummarizedExperimentFromGISTIC

Loading required package: dbplyr
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

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R.utils v2.12.0 (2022-06-28 03:20:05 UTC) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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    cat, commandArgs, getOption, isOpen, nullfile, parse, warnings

snapshotDate(): 2022-04-26
Working on: COAD_CNASeq-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
require("RaggedExperiment")
Working on: COAD_miRNASeqGene-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_mRNAArray-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_Mutation-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_Methylation_methyl27-20160128,
 COAD_Methylation_methyl450-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
require("rhdf5")
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

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Attaching package: 'DelayedArray'

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Attaching package: 'HDF5Array'

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Working on: COAD_Methylation_methyl27-20160128,
 COAD_Methylation_methyl450-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 3545 sampleMap rows not in names(experiments)

Attaching package: 'AnnotationHub'

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snapshotDate(): 2022-04-25
Quitting from lines 374-382 (TCGAutils.Rmd) 
Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics:
failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/"

--- failed re-building 'TCGAutils.Rmd'

SUMMARY: processing the following file failed:
  'TCGAutils.Rmd'

Error: Vignette re-building failed.
Execution halted