##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data XNAString
###
##############################################################################
##############################################################################


* checking for file ‘XNAString/DESCRIPTION’ ... OK
* preparing ‘XNAString’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘XNAString_vignette.Rmd’ using rmarkdown

Quitting from XNAString_vignette.Rmd:648-658 [unnamed-chunk-34]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'start': pattern() has moved from Biostrings to the pwalign package, and is formally
  defunct in Biostrings >= 2.77.1. Please call pwalign::pattern() to get rid of
  this error.
---
Backtrace:
    ▆
 1. ├─XNAString::XNAStringToHelm(obj)
 2. │ ├─base::paste(...)
 3. │ └─XNAString::siRNA_HELM(xnastring_obj)
 4. │   ├─Biostrings::start(Biostrings::pattern(pa))
 5. │   └─Biostrings::pattern(pa)
 6. │     └─Biostrings:::.call_fun_in_pwalign("pattern", ...)
 7. │       └─base::.Defunct(msg = wmsg(msg))
 8. │         └─base::stop(...)
 9. └─base (local) `<fn>`(`<dfnctErr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'XNAString_vignette.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'start': pattern() has moved from Biostrings to the pwalign package, and is formally
  defunct in Biostrings >= 2.77.1. Please call pwalign::pattern() to get rid of
  this error.
--- failed re-building ‘XNAString_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘XNAString_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted