############################################################################## ############################################################################## ### ### 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