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### Running command:
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###   chmod a+r genomicInstability -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data genomicInstability
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* checking for file 'genomicInstability/DESCRIPTION' ... OK
* preparing 'genomicInstability':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'genomicInstability.Rnw' using Sweave
Loading required package: checkmate
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    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'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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    findMatches

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    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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'

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

    rowMedians

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    anyMissing, rowMedians

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

    anyMissing

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    cache

GSE103322 not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Generating the genesets from the genome information
Computing the enrichment for the genesets in the expression matrix
Generating the genesets from the genome information
Computing the enrichment for the genesets in the expression matrix
Computing null model
Estimating the normalized enrichment scores
Type 'citation("pROC")' for a citation.

Attaching package: 'pROC'

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

    cov, var

The following objects are masked from 'package:S4Vectors':

    cov, var

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

    var

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

    cov, smooth, var

Setting levels: control = 0, case = 1
Setting direction: controls < cases
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "genomicInstability.tex" ' had status 1033
Error: processing vignette 'genomicInstability.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'genomicInstability.pdf' for vignette with name 'genomicInstability' and engine 'utils::Sweave'. The following files exist in working directory 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpQBBZeg\Rbuild5485b356e5a\genomicInstability\vignettes': 'genomicInstability-concordance.tex' (680 bytes), 'genomicInstability-density.pdf' (7308 bytes), 'genomicInstability-fit.pdf' (14268 bytes), 'genomicInstability-fitClass.pdf' (24337 bytes), 'genomicInstability-fitNull.pdf' (18143 bytes), 'genomicInstability-likelihood.pdf' (16967 bytes), 'genomicInstability-roc.pdf' (6083 bytes), 'genomicInstability.Rnw' (22279 bytes), 'genomicInstability.tex' (27233 bytes), 'heatmap.png' (454278 bytes)
--- failed re-building 'genomicInstability.Rnw'

SUMMARY: processing the following file failed:
  'genomicInstability.Rnw'

Error: Vignette re-building failed.
Execution halted