############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD build --keep-empty-dirs --no-resave-data Single.mTEC.Transcriptomes ### ############################################################################## ############################################################################## * checking for file ‘Single.mTEC.Transcriptomes/DESCRIPTION’ ... OK * preparing ‘Single.mTEC.Transcriptomes’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘mTECs.Rnw’ using knitr Loading required package: S4Vectors 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb 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: 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 Loading required package: AnnotationDbi Attaching package: 'genefilter' The following objects are masked from 'package:MatrixGenerics': rowSds, rowVars The following objects are masked from 'package:matrixStats': rowSds, rowVars gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: 'gdata' The following object is masked from 'package:SummarizedExperiment': trim The following object is masked from 'package:Biobase': combine The following object is masked from 'package:GenomicRanges': trim The following objects are masked from 'package:IRanges': startsWith, trim The following objects are masked from 'package:S4Vectors': first, first<- The following object is masked from 'package:BiocGenerics': combine The following object is masked from 'package:stats4': nobs The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith Registered S3 method overwritten by 'gplots': method from reorder.factor gdata Attaching package: 'gplots' The following object is masked from 'package:gdata': reorder.factor The following object is masked from 'package:IRanges': space The following object is masked from 'package:S4Vectors': space The following object is masked from 'package:stats': lowess Attaching package: 'gridExtra' The following object is masked from 'package:gdata': combine The following object is masked from 'package:Biobase': combine The following object is masked from 'package:BiocGenerics': combine This package provides documented data and code to reproduce the results and figures from the manuscript: Brennecke et al. Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. Nature Immunology 16,933-941 (2015) doi:10.1038/ni.3246 Loading required package: lattice Loading required package: annotate Loading required package: XML Warning: Removed 77 rows containing non-finite values (stat_ydensity). Warning: Removed 77 rows containing non-finite values (stat_boxplot). Warning: Removed 8 rows containing non-finite values (stat_ydensity). Warning: Removed 8 rows containing non-finite values (stat_boxplot). Warning: Removed 3 rows containing non-finite values (stat_ydensity). Warning: Removed 3 rows containing non-finite values (stat_boxplot). Warning: Removed 28 rows containing missing values (geom_point). Registered S3 method overwritten by 'GGally': method from +.gg ggplot2 Need specific help about ggbio? try mailing the maintainer or visit https://lawremi.github.io/ggbio/ Attaching package: 'ggbio' The following objects are masked from 'package:ggplot2': geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning: Ignoring unknown parameters: fill Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Attaching package: 'Gviz' The following object is masked from 'package:geneplotter': imageMap Quitting from lines 2898-2933 (mTECs.Rnw) Error: processing vignette 'mTECs.Rnw' failed with diagnostics: Can't add `e2` to a ggplot object. --- failed re-building ‘mTECs.Rnw’ SUMMARY: processing the following file failed: ‘mTECs.Rnw’ Error: Vignette re-building failed. Execution halted