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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 dce
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* checking for file ‘dce/DESCRIPTION’ ... OK
* preparing ‘dce’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dce.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: MultiAssayExperiment
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: GenomicRanges
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, 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:base':

    I, expand.grid, unname

Loading required package: IRanges
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


Attaching package: 'TCGAutils'

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

    splitAssays

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ tibble  3.1.8      ✔ dplyr   1.0.10
✔ tidyr   1.2.1      ✔ stringr 1.4.1 
✔ readr   2.1.3      ✔ forcats 0.5.2 
✔ purrr   0.3.5      
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position()
✖ dplyr::collapse()        masks IRanges::collapse()
✖ dplyr::combine()         masks Biobase::combine(), BiocGenerics::combine()
✖ dplyr::count()           masks matrixStats::count()
✖ dplyr::desc()            masks IRanges::desc()
✖ tidyr::expand()          masks S4Vectors::expand()
✖ dplyr::filter()          masks stats::filter()
✖ dplyr::first()           masks S4Vectors::first()
✖ dplyr::lag()             masks stats::lag()
✖ purrr::reduce()          masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename()          masks S4Vectors::rename()
✖ dplyr::slice()           masks IRanges::slice()

Attaching package: 'graph'

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

    boundary


Registered S3 methods overwritten by 'RcppEigen':
  method               from         
  predict.fastLm       RcppArmadillo
  print.fastLm         RcppArmadillo
  summary.fastLm       RcppArmadillo
  print.summary.fastLm RcppArmadillo
Quitting from lines 74-83 (dce.Rmd) 
Error: processing vignette 'dce.Rmd' failed with diagnostics:
unused argument (na.value = 0.2)
--- failed re-building ‘dce.Rmd’

--- re-building ‘pathway_databases.Rmd’ using rmarkdown
INFO [2022-10-18 17:58:44] Processing pathbank
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
INFO [2022-10-18 17:59:15] Processing kegg
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Quitting from lines 64-80 (pathway_databases.Rmd) 
Error: processing vignette 'pathway_databases.Rmd' failed with diagnostics:
unused argument (na.value = 0.2)
--- failed re-building ‘pathway_databases.Rmd’

SUMMARY: processing the following files failed:
  ‘dce.Rmd’ ‘pathway_databases.Rmd’

Error: Vignette re-building failed.
Execution halted