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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 TCGAWorkflow
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* checking for file ‘TCGAWorkflow/DESCRIPTION’ ... OK
* preparing ‘TCGAWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘TCGAWorkflow.Rmd’ using rmarkdown
Warning: replacing previous import 'SummarizedExperiment::as.data.frame' by 'motifStack::as.data.frame' when loading 'TCGAWorkflow'
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

--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
--------------------
oo Filtering results
--------------------
ooo By file.type
ooo By barcode
----------------
oo Checking data
----------------
ooo Checking if there are duplicated cases
ooo Checking if there are results for the query
-------------------
o Preparing output
-------------------
Downloading data for project TCGA-GBM
GDCdownload will download 2 files. A total of 60.483 KB
Downloading as: Tue_Oct_18_08_15_34_2022.tar.gz
To get the following information please change the clinical.info argument
=> new_tumor_events: new_tumor_event 
=> drugs: drug 
=> follow_ups: follow_up 
=> radiations: radiation
Parsing follow up version: follow_up_v1.0
Warning: `funs()` was deprecated in dplyr 0.8.0.
ℹ Please use a list of either functions or lambdas:

# Simple named list: list(mean = mean, median = median)

# Auto named with `tibble::lst()`: tibble::lst(mean, median)

# Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
ℹ The deprecated feature was likely used in the TCGAbiolinks package.
  Please report the issue at
  <https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues>.
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
Looking for clinical data in annoatation slot of MAF..
Number of mutated samples for given genes: 
Median survival..
Quitting from lines 818-825 (TCGAWorkflow.Rmd) 
Error: processing vignette 'TCGAWorkflow.Rmd' failed with diagnostics:
Time variable is not numeric
--- failed re-building ‘TCGAWorkflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted