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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data dearseq
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* checking for file ‘dearseq/DESCRIPTION’ ... OK
* preparing ‘dearseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dearseqUserguide.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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Reading file....
Parsing....
Found 55 entities...
GPL20301 (1 of 56 entities)
GSM2886035 (2 of 56 entities)
GSM2886036 (3 of 56 entities)
GSM2886037 (4 of 56 entities)
GSM2886038 (5 of 56 entities)
GSM2886039 (6 of 56 entities)
GSM2886040 (7 of 56 entities)
GSM2886041 (8 of 56 entities)
GSM2886042 (9 of 56 entities)
GSM2886043 (10 of 56 entities)
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GSM2886045 (12 of 56 entities)
GSM2886046 (13 of 56 entities)
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GSM2886073 (40 of 56 entities)
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GSM2886075 (42 of 56 entities)
GSM2886076 (43 of 56 entities)
GSM2886077 (44 of 56 entities)
GSM2886078 (45 of 56 entities)
GSM2886079 (46 of 56 entities)
GSM2886080 (47 of 56 entities)
GSM2886081 (48 of 56 entities)
GSM2886082 (49 of 56 entities)
GSM2886083 (50 of 56 entities)
GSM2886084 (51 of 56 entities)
GSM2886085 (52 of 56 entities)
GSM2886086 (53 of 56 entities)
GSM2886087 (54 of 56 entities)
GSM2886088 (55 of 56 entities)
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107991/suppl//GSE107991_edgeR_normalized_Berry_London.xlsx?tool=geoquery'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 9111773 bytes (8.7 MB)
==================================================
downloaded 8.7 MB

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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: 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
Loading required package: GenomeInfoDb
Quitting from lines 186-212 (dearseqUserguide.Rmd) 
Error: processing vignette 'dearseqUserguide.Rmd' failed with diagnostics:
there is no package called 'edgeR'
--- failed re-building ‘dearseqUserguide.Rmd’

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

Error: Vignette re-building failed.
Execution halted