build-last-errors="[]"
build-last-errors-base-dir="D:/Dropbox/rstudio/github/bioconductor/vulcan/"
build-last-outputs="[{\"output\":\"==> Rcmd.exe INSTALL --no-multiarch --with-keep.source vulcan\\n\\n\",\"type\":0},{\"output\":\"* installing to library 'D:/Programs/R-3.4.1/library'\\r\\n\",\"type\":1},{\"output\":\"* installing *source* package 'vulcan' ...\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\r\\n\",\"type\":1},{\"output\":\"** inst\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** preparing package for lazy loading\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** building package indices\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\r\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* DONE (vulcan)\\r\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
compile_pdf_state="{\"errors\":[],\"output\":\"Writing to file vulcan.tex\\r\\nProcessing code chunks with options ...\\r\\n 1 : keep.source term hide (vulcan.Rnw:62)\\r\\n 2 : echo keep.source (vulcan.Rnw:66)\\r\\n 3 : echo keep.source term hide (vulcan.Rnw:75)\\r\\nLoading required package: IRanges\\r\\nLoading required package: BiocGenerics\\r\\nLoading required package: parallel\\r\\n\\r\\nAttaching package: 'BiocGenerics'\\r\\n\\r\\nThe following objects are masked from 'package:parallel':\\r\\n\\r\\n    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\\r\\n    clusterExport, clusterMap, parApply, parCapply, parLapply,\\r\\n    parLapplyLB, parRapply, parSapply, parSapplyLB\\r\\n\\r\\nThe following objects are masked from 'package:stats':\\r\\n\\r\\n    IQR, mad, sd, var, xtabs\\r\\n\\r\\nThe following objects are masked from 'package:base':\\r\\n\\r\\n    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,\\r\\n    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\\r\\n    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,\\r\\n    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\\r\\n    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,\\r\\n    table, tapply, union, unique, unsplit, which, which.max, which.min\\r\\n\\r\\nLoading required package: S4Vectors\\r\\nLoading required package: stats4\\r\\n\\r\\nAttaching package: 'S4Vectors'\\r\\n\\r\\nThe following object is masked from 'package:base':\\r\\n\\r\\n    expand.grid\\r\\n\\r\\nLoading required package: DiffBind\\r\\nLoading required package: GenomicRanges\\r\\nLoading required package: GenomeInfoDb\\r\\nLoading required package: SummarizedExperiment\\r\\nLoading required package: Biobase\\r\\nWelcome to Bioconductor\\r\\n\\r\\n    Vignettes contain introductory material; view with\\r\\n    'browseVignettes()'. To cite Bioconductor, see\\r\\n    'citation(\\\"Biobase\\\")', and for packages 'citation(\\\"pkgname\\\")'.\\r\\n\\r\\nLoading required package: DelayedArray\\r\\nLoading required package: matrixStats\\r\\n\\r\\nAttaching package: 'matrixStats'\\r\\n\\r\\nThe following objects are masked from 'package:Biobase':\\r\\n\\r\\n    anyMissing, rowMedians\\r\\n\\r\\n\\r\\nAttaching package: 'DelayedArray'\\r\\n\\r\\nThe following objects are masked from 'package:matrixStats':\\r\\n\\r\\n    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges\\r\\n\\r\\nThe following object is masked from 'package:base':\\r\\n\\r\\n    apply\\r\\n\\r\\n\\r\\nLoading required package: viper\\r\\nLoading required package: ChIPpeakAnno\\r\\nLoading required package: grid\\r\\nLoading required package: Biostrings\\r\\nLoading required package: XVector\\r\\n\\r\\nAttaching package: 'Biostrings'\\r\\n\\r\\nThe following object is masked from 'package:DelayedArray':\\r\\n\\r\\n    type\\r\\n\\r\\nThe following object is masked from 'package:base':\\r\\n\\r\\n    strsplit\\r\\n\\r\\nLoading required package: VennDiagram\\r\\nLoading required package: futile.logger\\r\\nLoading required package: gplots\\r\\n\\r\\nAttaching package: 'gplots'\\r\\n\\r\\nThe following object is masked from 'package:IRanges':\\r\\n\\r\\n    space\\r\\n\\r\\nThe following object is masked from 'package:S4Vectors':\\r\\n\\r\\n    space\\r\\n\\r\\nThe following object is masked from 'package:stats':\\r\\n\\r\\n    lowess\\r\\n\\r\\nLoading required package: TxDb.Hsapiens.UCSC.hg19.knownGene\\r\\nLoading required package: GenomicFeatures\\r\\nLoading required package: AnnotationDbi\\r\\nLoading required package: DESeq\\r\\nLoading required package: locfit\\r\\nlocfit 1.5-9.1 \\t 2013-03-22\\r\\nLoading required package: lattice\\r\\n    Welcome to 'DESeq'. For improved performance, usability and\\r\\n    functionality, please consider migrating to 'DESeq2'.\\r\\nLoading required package: zoo\\r\\n\\r\\nAttaching package: 'zoo'\\r\\n\\r\\nThe following objects are masked from 'package:base':\\r\\n\\r\\n    as.Date, as.Date.numeric\\r\\n\\r\\nLoading required package: wordcloud\\r\\nLoading required package: RColorBrewer\\r\\n\\r\\nAttaching package: 'wordcloud'\\r\\n\\r\\nThe following object is masked from 'package:gplots':\\r\\n\\r\\n    textplot\\r\\n\\r\\nLoading required package: csaw\\r\\nLoading required package: BiocParallel\\r\\nLoading required package: caTools\\r\\n\\r\\nAttaching package: 'caTools'\\r\\n\\r\\nThe following object is masked from 'package:IRanges':\\r\\n\\r\\n    runmean\\r\\n\\r\\nThe following object is masked from 'package:S4Vectors':\\r\\n\\r\\n    runmean\\r\\n\\r\\n\\r\\nAttaching package: 'vulcan'\\r\\n\\r\\nThe following object is masked from 'package:XVector':\\r\\n\\r\\n    slice\\r\\n\\r\\nThe following object is masked from 'package:IRanges':\\r\\n\\r\\n    slice\\r\\n\\r\\n 4 : echo keep.source term hide (vulcan.Rnw:80)\\r\\n 5 : echo keep.source term hide (vulcan.Rnw:88)\\r\\n 6 : echo keep.source term hide (vulcan.Rnw:95)\\r\\nT90_1 MCF7 ER t90  1 bed\\r\\nT90_2 MCF7 ER t90  2 bed\\r\\nT90_3 MCF7 ER t90  3 bed\\r\\nT90_4 MCF7 ER t90  4 bed\\r\\nT45_1 MCF7 ER t45  1 bed\\r\\nT45_2 MCF7 ER t45  2 bed\\r\\nT45_3 MCF7 ER t45  3 bed\\r\\nT45_4 MCF7 ER t45  4 bed\\r\\nT0_1 MCF7 ER t0  1 bed\\r\\nT0_2 MCF7 ER t0  2 bed\\r\\nT0_3 MCF7 ER t0  3 bed\\r\\nT0_4 MCF7 ER t0  4 bed\\r\\nSheet loaded. You have 12 samples and 3 conditions\\r\\nPeak size automatically detected as 334nt\\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/A90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/B90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/C90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/D90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/A45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/B45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/C45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/D45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/A0_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/B0_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/C0_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/D0_I.bam125 \\r\\nRe-centering peaks...\\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/A90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/B90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/C90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/D90_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/A45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/B45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/C45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/D45_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/A0_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/B0_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/C0_I.bam125 \\r\\nSample: D:/Programs/R-3.4.1/library/vulcandata/extdata/D0_I.bam125 \\r\\n 7 : echo keep.source term hide (vulcan.Rnw:102)\\r\\nAnnotate peaks by annoPeaks, see ?annoPeaks for details.\\r\\nmaxgap will be ignored.\\r\\nAnnotate peaks by annoPeaks, see ?annoPeaks for details.\\r\\nmaxgap will be ignored.\\r\\n 8 : echo keep.source term hide (vulcan.Rnw:108)\\r\\n 9 : echo keep.source term hide (vulcan.Rnw:118)\\r\\n10 : echo keep.source term hide pdf  (vulcan.Rnw:128)\\r\\nThu Oct 26 12:52:25 2017\\r\\nComputing the null model distribution by 1000 permutations.\\r\\n-------\\r\\nThu Oct 26 12:52:25 2017\\r\\nComputing regulon enrichment with aREA algorithm\\r\\n\\r\\nEstimating the normalized enrichment scores\\r\\n11 : echo keep.source term hide (vulcan.Rnw:143)\\r\\n12 : echo keep.source term hide pdf  (vulcan.Rnw:150)\\r\\n13 : echo keep.source term hide (vulcan.Rnw:158)\\r\\n14 : echo keep.source term hide pdf  (vulcan.Rnw:172)\\r\\n\\r\\nYou can now run (pdf)latex on 'vulcan.tex'\\r\\nWarning messages:\\r\\n1: In dba.multicore.init(DBA$config) :\\r\\n  Parallel execution unavailable: executing serially.\\r\\n2: In dba.parallel(pv) : UNKNOWN PARALLEL PACKAGE: 0\\r\\nRunning pdflatex.exe on vulcan.tex...completed\\n\\nCreated PDF: D:/Dropbox/rstudio/github/bioconductor/vulcan/vignettes/vulcan.pdf\\n\",\"running\":false,\"tab_visible\":true,\"target_file\":\"D:/Dropbox/rstudio/github/bioconductor/vulcan/vignettes/vulcan.Rnw\"}"
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