##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAutils
###
##############################################################################
##############################################################################
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* preparing ‘TCGAutils’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘TCGAutils.Rmd’ using rmarkdown
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: 'MultiAssayExperiment'
The following object is masked from 'package:TCGAutils':
splitAssays
Attaching package: 'RTCGAToolbox'
The following object is masked from 'package:TCGAutils':
makeSummarizedExperimentFromGISTIC
Loading required package: dbplyr
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following object is masked from 'package:R.methodsS3':
throw
The following object is masked from 'package:SummarizedExperiment':
trim
The following object is masked from 'package:GenomicRanges':
trim
The following object is masked from 'package:IRanges':
trim
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, load, save
R.utils v2.12.0 (2022-06-28 03:20:05 UTC) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, isOpen, nullfile, parse, warnings
snapshotDate(): 2022-04-26
Working on: COAD_CNASeq-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
require("RaggedExperiment")
Working on: COAD_miRNASeqGene-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_mRNAArray-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_Mutation-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_Methylation_methyl27-20160128,
COAD_Methylation_methyl450-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
require("rhdf5")
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
Attaching package: 'HDF5Array'
The following object is masked from 'package:rhdf5':
h5ls
Working on: COAD_Methylation_methyl27-20160128,
COAD_Methylation_methyl450-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
removing 3545 sampleMap rows not in names(experiments)
Attaching package: 'AnnotationHub'
The following object is masked from 'package:rtracklayer':
hubUrl
The following object is masked from 'package:Biobase':
cache
snapshotDate(): 2022-04-25
Quitting from lines 374-382 (TCGAutils.Rmd)
Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics:
failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/"
--- failed re-building ‘TCGAutils.Rmd’
SUMMARY: processing the following file failed:
‘TCGAutils.Rmd’
Error: Vignette re-building failed.
Execution halted