############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 universalmotif ### ############################################################################## ############################################################################## * checking for file ‘universalmotif/DESCRIPTION’ ... OK * preparing ‘universalmotif’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Introduction.Rmd’ using rmarkdown --- finished re-building ‘Introduction.Rmd’ --- re-building ‘IntroductionToSequenceMotifs.Rmd’ using rmarkdown --- finished re-building ‘IntroductionToSequenceMotifs.Rmd’ --- re-building ‘MotifComparisonAndPvalues.Rmd’ using rmarkdown --- finished re-building ‘MotifComparisonAndPvalues.Rmd’ --- re-building ‘MotifManipulation.Rmd’ using rmarkdown --- finished re-building ‘MotifManipulation.Rmd’ --- re-building ‘SequenceSearches.Rmd’ using rmarkdown Quitting from SequenceSearches.Rmd:374-404 [unnamed-chunk-20] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `validObject()`: ! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL" --- Backtrace: x 1. +-ggplot2::autoplot(...) 2. \-ggbio::autoplot(...) 3. \-ggbio (local) .local(object, ...) 4. \-ggbio::GGbio(p, data = object) 5. +-BiocGenerics::do.call(...) 6. +-base::do.call(...) 7. \-methods (local) ``(...) 8. +-methods::initialize(value, ...) 9. \-methods::initialize(value, ...) 10. \-methods::validObject(.Object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'SequenceSearches.Rmd' failed with diagnostics: invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL" --- failed re-building ‘SequenceSearches.Rmd’ SUMMARY: processing the following file failed: ‘SequenceSearches.Rmd’ Error: Vignette re-building failed. Execution halted