############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 factR ### ############################################################################## ############################################################################## * checking for file ‘factR/DESCRIPTION’ ... OK * preparing ‘factR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘factR.Rmd’ using rmarkdown trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz' Content type 'unknown' length 28542432 bytes (27.2 MB) ================================================== Quitting from factR.Rmd:318-320 [viewafterCDS] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `h()`: ! error in evaluating the argument 'args' in selecting a method for function 'do.call': object 'ccds' not found --- Backtrace: ▆ 1. ├─factR::viewTranscripts(custom_new_CDS.gtf, "Zfr") 2. │ ├─BiocGenerics::do.call(...) 3. │ └─base::lapply(...) 4. │ └─factR (local) FUN(X[[i]], ...) 5. │ ├─base::suppressWarnings(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ └─wiggleplotr::plotTranscripts(...) 8. └─base::.handleSimpleError(...) 9. └─base (local) h(simpleError(msg, call)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'factR.Rmd' failed with diagnostics: error in evaluating the argument 'args' in selecting a method for function 'do.call': object 'ccds' not found --- failed re-building ‘factR.Rmd’ SUMMARY: processing the following file failed: ‘factR.Rmd’ Error: Vignette re-building failed. Execution halted