############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r miloR -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data miloR ### ############################################################################## ############################################################################## * checking for file 'miloR/DESCRIPTION' ... OK * preparing 'miloR': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'milo_demo.Rmd' using rmarkdown Loading required package: edgeR Loading required package: limma 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 object is masked from 'package:limma': plotMA 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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: 'SingleCellExperiment' The following object is masked from 'package:edgeR': cpm Loading required package: scuttle Loading required package: ggplot2 Attaching package: 'scater' The following object is masked from 'package:limma': plotMDS Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:GenomicRanges': intersect, setdiff, union The following object is masked from 'package:GenomeInfoDb': intersect The following objects are masked from 'package:IRanges': collapse, desc, intersect, setdiff, slice, union The following objects are masked from 'package:S4Vectors': first, intersect, rename, setdiff, setequal, union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following object is masked from 'package:matrixStats': count The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union --- finished re-building 'milo_demo.Rmd' --- re-building 'milo_gastrulation.Rmd' using rmarkdown Loading required package: SpatialExperiment snapshotDate(): 2021-10-19 see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation loading from cache Constructing kNN graph with k:30 Checking valid object Checking meta.data validity Counting cells in neighbourhoods Using TMM normalisation Performing spatial FDR correction withk-distance weighting Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider increasing max.overlaps Converting celltype to factor... Converting group.by to factor... Found 325 DA neighbourhoods at FDR 10% nhoodAdjacency found - using for nhood grouping Converting group.by to factor... Found 325 DA neighbourhoods at FDR 10% nhoodAdjacency found - using for nhood grouping Converting group.by to factor... Quitting from lines 397-402 (milo_gastrulation.Rmd) Error: processing vignette 'milo_gastrulation.Rmd' failed with diagnostics: contrasts can be applied only to factors with 2 or more levels --- failed re-building 'milo_gastrulation.Rmd' SUMMARY: processing the following file failed: 'milo_gastrulation.Rmd' Error: Vignette re-building failed. Execution halted