############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scmeth ### ############################################################################## ############################################################################## * checking for file ‘scmeth/DESCRIPTION’ ... OK * preparing ‘scmeth’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘my-vignette.Rmd’ using rmarkdown Quitting from my-vignette.Rmd:166-170 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `h()`: ! error in evaluating the argument 'i' in selecting a method for function '[[': 'organism' is not an exported object from 'namespace:GenomeInfoDb' --- Backtrace: ▆ 1. ├─scmeth::repMask(bs, Mmusculus, "mm10") 2. │ ├─...[[]] 3. │ ├─AnnotationHub::query(...) 4. │ └─AnnotationHub::query(...) 5. │ └─AnnotationHub (local) .local(x, pattern, ...) 6. └─base::.handleSimpleError(...) 7. └─base (local) h(simpleError(msg, call)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: error in evaluating the argument 'i' in selecting a method for function '[[': 'organism' is not an exported object from 'namespace:GenomeInfoDb' --- failed re-building ‘my-vignette.Rmd’ SUMMARY: processing the following file failed: ‘my-vignette.Rmd’ Error: Vignette re-building failed. Execution halted