############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data VariantAnnotation ### ############################################################################## ############################################################################## * checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK * preparing ‘VariantAnnotation’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘VariantAnnotation.Rmd’ using rmarkdown [W::bcf_hdr_check_sanity] GL should be declared as Number=G --- finished re-building ‘VariantAnnotation.Rmd’ --- re-building ‘ensemblVEP.Rmd’ using rmarkdown --- finished re-building ‘ensemblVEP.Rmd’ --- re-building ‘filterVcf.Rmd’ using rmarkdown Quitting from filterVcf.Rmd:209-214 [mcf7regulatoryRegions] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'AnnotationHub' --- Backtrace: ▆ 1. └─base::library(AnnotationHub) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'filterVcf.Rmd' failed with diagnostics: there is no package called 'AnnotationHub' --- failed re-building ‘filterVcf.Rmd’ SUMMARY: processing the following file failed: ‘filterVcf.Rmd’ Error: Vignette re-building failed. Execution halted