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### Running command:
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###   chmod a+r ELMER -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ELMER
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* checking for file 'ELMER/DESCRIPTION' ... OK
* preparing 'ELMER':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'analysis_data_input.Rmd' using rmarkdown
Loading required package: ELMER.data

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 54-60 (analysis_data_input.Rmd) 
Error: processing vignette 'analysis_data_input.Rmd' failed with diagnostics:
Data HM450.hg19.manifest not found.

--- failed re-building 'analysis_data_input.Rmd'

--- re-building 'analysis_diff_meth.Rmd' using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'mae.rda', probable reason 'No such file or directory'
Quitting from lines 69-80 (analysis_diff_meth.Rmd) 
Error: processing vignette 'analysis_diff_meth.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'analysis_diff_meth.Rmd'

--- re-building 'analysis_get_pair.Rmd' using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'mae.rda', probable reason 'No such file or directory'
Quitting from lines 109-133 (analysis_get_pair.Rmd) 
Error: processing vignette 'analysis_get_pair.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'analysis_get_pair.Rmd'

--- re-building 'analysis_gui.Rmd' using rmarkdown
--- finished re-building 'analysis_gui.Rmd'

--- re-building 'analysis_motif_enrichment.Rmd' using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'mae.rda', probable reason 'No such file or directory'
Quitting from lines 68-82 (analysis_motif_enrichment.Rmd) 
Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'analysis_motif_enrichment.Rmd'

--- re-building 'analysis_regulatory_tf.Rmd' using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'mae.rda', probable reason 'No such file or directory'
Quitting from lines 87-90 (analysis_regulatory_tf.Rmd) 
Error: processing vignette 'analysis_regulatory_tf.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'analysis_regulatory_tf.Rmd'

--- re-building 'index.Rmd' using rmarkdown
--- finished re-building 'index.Rmd'

--- re-building 'input.Rmd' using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    count


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:dplyr':

    combine, intersect, setdiff, union

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    first, rename

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

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

    anyMissing, rowMedians

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Quitting from lines 133-188 (input.Rmd) 
Error: processing vignette 'input.Rmd' failed with diagnostics:
Data HM450.hg19.manifest not found.

--- failed re-building 'input.Rmd'

--- re-building 'pipe.Rmd' using rmarkdown
--- finished re-building 'pipe.Rmd'

--- re-building 'plots_TF.Rmd' using rmarkdown
Quitting from lines 41-46 (plots_TF.Rmd) 
Error: processing vignette 'plots_TF.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'plots_TF.Rmd'

--- re-building 'plots_heatmap.Rmd' using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'mae.rda', probable reason 'No such file or directory'
Quitting from lines 33-35 (plots_heatmap.Rmd) 
Error: processing vignette 'plots_heatmap.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building 'plots_heatmap.Rmd'

--- re-building 'plots_motif_enrichment.Rmd' using rmarkdown
Quitting from lines 36-40 (plots_motif_enrichment.Rmd) 
Error: processing vignette 'plots_motif_enrichment.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'plots_motif_enrichment.Rmd'

--- re-building 'plots_scatter.Rmd' using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'mae.rda', probable reason 'No such file or directory'
Quitting from lines 33-35 (plots_scatter.Rmd) 
Error: processing vignette 'plots_scatter.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building 'plots_scatter.Rmd'

--- re-building 'plots_schematic.Rmd' using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'mae.rda', probable reason 'No such file or directory'
Quitting from lines 32-35 (plots_schematic.Rmd) 
Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building 'plots_schematic.Rmd'

--- re-building 'usecase.Rmd' using rmarkdown
--- finished re-building 'usecase.Rmd'

SUMMARY: processing the following files failed:
  'analysis_data_input.Rmd' 'analysis_diff_meth.Rmd'
  'analysis_get_pair.Rmd' 'analysis_motif_enrichment.Rmd'
  'analysis_regulatory_tf.Rmd' 'input.Rmd' 'plots_TF.Rmd'
  'plots_heatmap.Rmd' 'plots_motif_enrichment.Rmd' 'plots_scatter.Rmd'
  'plots_schematic.Rmd'

Error: Vignette re-building failed.
Execution halted