############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data ggbio ### ############################################################################## ############################################################################## * checking for file ‘ggbio/DESCRIPTION’ ... OK * preparing ‘ggbio’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘ggbio.Rnw’ using Sweave --- finished re-building ‘ggbio.Rnw’ cp realvignettes/*.Rnw . /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/Rscript -e "library(knitr); knit2pdf('ggbio.Rnw')" processing file: ggbio.Rnw 1/125 2/125 [style-knitr] 3/125 4/125 [setup] 5/125 6/125 [citation] 7/125 8/125 [unnamed-chunk-1] 9/125 10/125 [unnamed-chunk-2] 11/125 12/125 [unnamed-chunk-3] 13/125 14/125 [unnamed-chunk-4] Error in validObject(.Object) : invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL" Calls: knit2pdf ... -> initialize -> initialize -> validObject Quitting from ggbio.Rnw:107-114 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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. \-ggbio::Ideogram(genome = "hg19") 2. +-methods::new(...) 3. | +-methods::initialize(value, ...) 4. | \-methods::initialize(value, ...) 5. \-ggbio::ggbio(p, data = obj.ori, ...) 6. +-BiocGenerics::do.call(...) 7. +-base::do.call(...) 8. \-methods (local) ``(...) 9. +-methods::initialize(value, ...) 10. \-methods::initialize(value, ...) 11. \-methods::validObject(.Object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted make: *** [Makefile:15: ggbio.pdf] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted