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### Running command:
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###   chmod a+r GenomicRanges -R && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GenomicRanges
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* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* preparing 'GenomicRanges':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'GenomicRangesIntroduction.Rmd' using rmarkdown
Error: processing vignette 'GenomicRangesIntroduction.Rmd' failed with diagnostics:
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- failed re-building 'GenomicRangesIntroduction.Rmd'

--- re-building 'ExtendingGenomicRanges.Rnw' using Sweave
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'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
--- finished re-building 'ExtendingGenomicRanges.Rnw'

--- re-building 'GRanges_and_GRangesList_slides.Rnw' using Sweave
Warning in .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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: 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

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

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
--- finished re-building 'GRanges_and_GRangesList_slides.Rnw'

--- re-building 'GenomicRangesHOWTOs.Rnw' using Sweave

Attaching package: 'txdbmaker'

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

    UCSCFeatureDbTableSchema, browseUCSCtrack,
    getChromInfoFromBiomart, makeFDbPackageFromUCSC,
    makeFeatureDbFromUCSC, makePackageName, makeTxDb,
    makeTxDbFromBiomart, makeTxDbFromEnsembl, makeTxDbFromGFF,
    makeTxDbFromGRanges, makeTxDbFromUCSC, makeTxDbPackage,
    makeTxDbPackageFromBiomart, makeTxDbPackageFromUCSC,
    supportedMiRBaseBuildValues, supportedUCSCFeatureDbTables,
    supportedUCSCFeatureDbTracks, supportedUCSCtables

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features
  of type exon. This information was ignored.
OK
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    cache


Error: processing vignette 'GenomicRangesHOWTOs.Rnw' failed with diagnostics:
 chunk 29 (label = hub_1) 
Error : Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: C:\Users\biocbuild\AnnotationHub_cache
  filename: annotationhub.index.rds

--- failed re-building 'GenomicRangesHOWTOs.Rnw'

--- re-building 'Ten_things_slides.Rnw' using Sweave
Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

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

    hubUrl

--- finished re-building 'Ten_things_slides.Rnw'

SUMMARY: processing the following files failed:
  'GenomicRangesIntroduction.Rmd' 'GenomicRangesHOWTOs.Rnw'

Error: Vignette re-building failed.
Execution halted