############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data saseR ### ############################################################################## ############################################################################## * checking for file ‘saseR/DESCRIPTION’ ... OK * preparing ‘saseR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘saseR-vignette.Rmd’ using rmarkdown Quitting from saseR-vignette.Rmd:500-504 [unnamed-chunk-25] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `call_fun_in_txdbmaker()`: ! makeTxDbFromGFF() has moved from GenomicFeatures to the txdbmaker package, and is formally defunct in GenomicFeatures >= 1.61.1. Please call txdbmaker::makeTxDbFromGFF() to get rid of this error. --- Backtrace: ▆ 1. └─GenomicFeatures::makeTxDbFromGFF(gtfFileName) 2. └─GenomicFeatures:::call_fun_in_txdbmaker("makeTxDbFromGFF", ...) 3. └─base::.Defunct(msg = wmsg(msg)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'saseR-vignette.Rmd' failed with diagnostics: makeTxDbFromGFF() has moved from GenomicFeatures to the txdbmaker package, and is formally defunct in GenomicFeatures >= 1.61.1. Please call txdbmaker::makeTxDbFromGFF() to get rid of this error. --- failed re-building ‘saseR-vignette.Rmd’ SUMMARY: processing the following file failed: ‘saseR-vignette.Rmd’ Error: Vignette re-building failed. Execution halted