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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 glmSparseNet
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* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* preparing ‘glmSparseNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘example_brca_logistic.Rmd’ using rmarkdown

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

Loading required package: MultiAssayExperiment
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

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

Quitting from lines 28-42 (example_brca_logistic.Rmd) 
Error: processing vignette 'example_brca_logistic.Rmd' failed with diagnostics:
there is no package called 'TCGAutils'
--- failed re-building ‘example_brca_logistic.Rmd’

--- re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ using rmarkdown

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: grid
Quitting from lines 28-49 (example_brca_protein-protein-interactions_survival.Rmd) 
Error: processing vignette 'example_brca_protein-protein-interactions_survival.Rmd' failed with diagnostics:
there is no package called 'TCGAutils'
--- failed re-building ‘example_brca_protein-protein-interactions_survival.Rmd’

--- re-building ‘example_brca_survival.Rmd’ using rmarkdown
Quitting from lines 28-42 (example_brca_survival.Rmd) 
Error: processing vignette 'example_brca_survival.Rmd' failed with diagnostics:
there is no package called 'TCGAutils'
--- failed re-building ‘example_brca_survival.Rmd’

--- re-building ‘example_prad_survival.Rmd’ using rmarkdown
Quitting from lines 28-42 (example_prad_survival.Rmd) 
Error: processing vignette 'example_prad_survival.Rmd' failed with diagnostics:
there is no package called 'TCGAutils'
--- failed re-building ‘example_prad_survival.Rmd’

--- re-building ‘example_skcm_survival.Rmd’ using rmarkdown
Quitting from lines 28-42 (example_skcm_survival.Rmd) 
Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics:
there is no package called 'TCGAutils'
--- failed re-building ‘example_skcm_survival.Rmd’

--- re-building ‘separate2GroupsCox.Rmd’ using rmarkdown
Loading required package: glmnet
Loaded glmnet 4.1-4
--- finished re-building ‘separate2GroupsCox.Rmd’

SUMMARY: processing the following files failed:
  ‘example_brca_logistic.Rmd’
  ‘example_brca_protein-protein-interactions_survival.Rmd’
  ‘example_brca_survival.Rmd’ ‘example_prad_survival.Rmd’
  ‘example_skcm_survival.Rmd’

Error: Vignette re-building failed.
Execution halted