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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data YAPSA
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* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* preparing ‘YAPSA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘YAPSA.Rmd’ using rmarkdown
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

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The following objects are masked from 'package:base':

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    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

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Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
Registered S3 method overwritten by 'GGally':
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Registered S3 methods overwritten by 'proxy':
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  print.registry_field registry
  print.registry_entry registry
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:grid':

    pattern

The following object is masked from 'package:base':

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Loading required package: rtracklayer
pandoc-citeproc: reference ComplexHeatmap2015 not found
--- finished re-building ‘YAPSA.Rmd’

--- re-building ‘vignette_confidenceIntervals.Rmd’ using rmarkdown
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--- finished re-building ‘vignette_confidenceIntervals.Rmd’

--- re-building ‘vignette_exomes.Rmd’ using rmarkdown
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--- finished re-building ‘vignette_exomes.Rmd’

--- re-building ‘vignette_signature_specific_cutoffs.Rmd’ using rmarkdown
Warning: `offset` is deprecated, use `location` instead.
Warning: `offset` is deprecated, use `location` instead.
Warning: The label(s) tab:Table1 not found
--- finished re-building ‘vignette_signature_specific_cutoffs.Rmd’

--- re-building ‘vignette_stratifiedAnalysis.Rmd’ using rmarkdown
Warning: `offset` is deprecated, use `location` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Quitting from lines 301-306 (vignette_stratifiedAnalysis.Rmd) 
Error: processing vignette 'vignette_stratifiedAnalysis.Rmd' failed with diagnostics:
'posthoc.kruskal.nemenyi.test.default' is defunct.
Use 'PMCMRplus::kwAllPairsNemenyiTest' instead.
See help("Defunct") and help("PMCMR-defunct").
--- failed re-building ‘vignette_stratifiedAnalysis.Rmd’

--- re-building ‘vignettes_Indel.Rmd’ using rmarkdown
Warning: `offset` is deprecated, use `location` instead.
--- finished re-building ‘vignettes_Indel.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_stratifiedAnalysis.Rmd’

Error: Vignette re-building failed.
Execution halted