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### Running command:
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###   chmod a+r SummarizedBenchmark -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SummarizedBenchmark
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* checking for file 'SummarizedBenchmark/DESCRIPTION' ... OK
* preparing 'SummarizedBenchmark':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'CaseStudy-RNAseqQuantification.Rmd' using rmarkdown
Loading required package: tidyr
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,
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    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
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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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Package 'mclust' version 5.4.7
Type 'citation("mclust")' for citing this R package in publications.
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Attaching package: 'dplyr'

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--- finished re-building 'CaseStudy-RNAseqQuantification.Rmd'

--- re-building 'CaseStudy-SingleCellSimulation.Rmd' using rmarkdown

Attaching package: 'magrittr'

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Loading required package: SingleCellExperiment
snapshotDate(): 2021-05-18
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
Quitting from lines 47-54 (CaseStudy-SingleCellSimulation.Rmd) 
Error: processing vignette 'CaseStudy-SingleCellSimulation.Rmd' failed with diagnostics:
failed to load resource
  name: EH2569
  title: Fluidigm Tophat counts
  reason: unknown input format
--- failed re-building 'CaseStudy-SingleCellSimulation.Rmd'

--- re-building 'Feature-ErrorHandling.Rmd' using rmarkdown
--- finished re-building 'Feature-ErrorHandling.Rmd'

--- re-building 'Feature-Iterative.Rmd' using rmarkdown

Attaching package: 'limma'

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Attaching package: 'edgeR'

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converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
using 'ashr' for LFC shrinkage. If used in published research, please cite:
    Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
    https://doi.org/10.1093/biostatistics/kxw041
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
using 'ashr' for LFC shrinkage. If used in published research, please cite:
    Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
    https://doi.org/10.1093/biostatistics/kxw041
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Found already estimated performance metrics, replacing these
--- finished re-building 'Feature-Iterative.Rmd'

--- re-building 'Feature-Parallel.Rmd' using rmarkdown
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
--- finished re-building 'Feature-Parallel.Rmd'

--- re-building 'SummarizedBenchmark-ClassDetails.Rmd' using rmarkdown

Attaching package: 'iCOBRA'

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    score, score<-

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    score, score<-

--- finished re-building 'SummarizedBenchmark-ClassDetails.Rmd'

--- re-building 'SummarizedBenchmark-FullCaseStudy.Rmd' using rmarkdown
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
--- finished re-building 'SummarizedBenchmark-FullCaseStudy.Rmd'

--- re-building 'SummarizedBenchmark-Introduction.Rmd' using rmarkdown
Found already estimated performance metrics, replacing these
--- finished re-building 'SummarizedBenchmark-Introduction.Rmd'

SUMMARY: processing the following file failed:
  'CaseStudy-SingleCellSimulation.Rmd'

Error: Vignette re-building failed.
Execution halted