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### Running command:
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###   chmod a+r MEAL -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MEAL
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* checking for file 'MEAL/DESCRIPTION' ... OK
* preparing 'MEAL':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'MEAL.Rmd' using rmarkdown
Loading required package: Biobase
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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MultiDataSet
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    rowRanges

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.5 	 2022-03-01
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19

Quitting from lines 194-196 (MEAL.Rmd) 
Error: processing vignette 'MEAL.Rmd' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building 'MEAL.Rmd'

--- re-building 'caseExample.Rmd' using rmarkdown
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19

Attaching package: 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'

The following objects are masked from 'package:IlluminaHumanMethylation450kanno.ilmn12.hg19':

    Islands.UCSC, Locations, Manifest, Other, SNPs.132CommonSingle,
    SNPs.135CommonSingle, SNPs.137CommonSingle, SNPs.138CommonSingle,
    SNPs.141CommonSingle, SNPs.142CommonSingle, SNPs.144CommonSingle,
    SNPs.146CommonSingle, SNPs.147CommonSingle, SNPs.Illumina

Warning in createModel(set, model) :
  There are some missing values in the samples data. Only complete cases will be used.
Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Quitting from lines 157-158 (caseExample.Rmd) 
Error: processing vignette 'caseExample.Rmd' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building 'caseExample.Rmd'

SUMMARY: processing the following files failed:
  'MEAL.Rmd' 'caseExample.Rmd'

Error: Vignette re-building failed.
Execution halted