############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fcoex ### ############################################################################## ############################################################################## * checking for file ‘fcoex/DESCRIPTION’ ... OK * preparing ‘fcoex’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘fcoex.Rmd’ using rmarkdown 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 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 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 Created new fcoex object. Getting SU scores for each gene Running FCBF to find module headers Calculating adjacency matrix Trimming and getting modules from adjacency matrix 12 modules were found. Quitting from lines 130-143 (fcoex.Rmd) Error: processing vignette 'fcoex.Rmd' failed with diagnostics: object 'gmt_in' not found --- failed re-building ‘fcoex.Rmd’ --- re-building ‘fcoex_and_seurat.Rmd’ using rmarkdown Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Warning in xtfrm.data.frame(x) : cannot xtfrm data frames Quitting from lines 67-75 (fcoex_and_seurat.Rmd) Error: processing vignette 'fcoex_and_seurat.Rmd' failed with diagnostics: invalid 'nchars' argument --- failed re-building ‘fcoex_and_seurat.Rmd’ SUMMARY: processing the following files failed: ‘fcoex.Rmd’ ‘fcoex_and_seurat.Rmd’ Error: Vignette re-building failed. Execution halted