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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data girafe
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* checking for file ‘girafe/DESCRIPTION’ ... OK
* preparing ‘girafe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘girafe.Rnw’ using Sweave
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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: intervals

Attaching package: ‘intervals’

The following object is masked from ‘package:GenomicRanges’:

    reduce

The following object is masked from ‘package:IRanges’:

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The following object is masked from ‘package:S4Vectors’:

    expand

The following objects are masked from ‘package:BiocGenerics’:

    type, type<-

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

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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: 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: genomeIntervals
Loading required package: grid

Attaching package: ‘grid’

The following object is masked from ‘package:Biostrings’:

    pattern

No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’
Loading required package: org.Mm.eg.db
Warning in `organism<-`(`*tmp*`, value = "Mm") :
  An annotation package called 'org.Mm.eg.db' could not be found.
Please check whether 'Mm' is a valid organism name or install the package. Example organism identifiers are 'Hs' for Human and 'Mm' for Mouse. The annotation  packages can usually be obtained from the Bioconductor repositories. You may want to try:
BiocManager::install('org.Mm.eg.db')

Loading required package: org.Mm.eg.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘org.Mm.eg.db’

Error: processing vignette 'girafe.Rnw' failed with diagnostics:
 chunk 19 (label = examplePerWindow) 
Error in getChromLengths(object) : 
  No package called 'org.Mm.eg.db' found. Install this package or check wether the organism annotation of object is correct (e.g. 'Mm' or 'Hs')


--- failed re-building ‘girafe.Rnw’

pdflatex girafe
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdflatex)
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\T1/cmr/m/n/10.95 sem-bly: \T1/cmr/m/it/10.95 mm9\T1/cmr/m/n/10.95 ). This ob-j
ect has been cre-ated be-fore-hand[][][][][] and it is of class \T1/cmr/m/it/10
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!  ==> Fatal error occurred, no output PDF file produced!
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