############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Wrench ### ############################################################################## ############################################################################## * checking for file ‘Wrench/DESCRIPTION’ ... OK * preparing ‘Wrench’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘vignette.Rmd’ using rmarkdown Loading required package: metagenomeSeq Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: glmnet Loading required package: Matrix Loaded glmnet 4.1-4 Loading required package: RColorBrewer Loading required package: edgeR Loading required package: Wrench Loading required package: DESeq2 Warning: glm.fit: algorithm did not converge Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred Warning: glm.fit: algorithm did not converge Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred Warning: Partial NA coefficients for 8430 probe(s) Quitting from lines 86-103 (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: there is no package called 'edgeR' --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted