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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DominoEffect
###
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* checking for file ‘DominoEffect/DESCRIPTION’ ... OK
* preparing ‘DominoEffect’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Vignette.Rmd’ using rmarkdown
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain;format=fasta' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain;format=fasta' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain;format=fasta' length 655 bytes
==================================================
downloaded 655 bytes


Quitting from Vignette.Rmd:60-63 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.call_fun_in_pwalign()`:
! 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. └─DominoEffect::DominoEffect(...)
 2.   └─DominoEffect::map_to_func_elem(results, write_to_file, ens_release = ens_release)
 3.     └─DominoEffect::align_to_unip(ens.seq, uni.seq, ensembl_mut_position)
 4.       ├─base::grep("-", pattern(alignment.subseq[1]))
 5.       │ └─base::is.factor(x)
 6.       └─Biostrings::pattern(alignment.subseq[1])
 7.         └─Biostrings:::.call_fun_in_pwalign("pattern", ...)
 8.           └─base::.Defunct(msg = wmsg(msg))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
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 ‘Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted