##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 LinTInd
###
##############################################################################
##############################################################################


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

Quitting from tutorial.Rmd:70-73 [find indels and generate array-form strings]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `checkForRemoteErrors()`:
! one node produced an error: error in evaluating the argument 'subject' in selecting a method for function 'matchPattern': 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. └─LinTInd::FindIndel(...)
 2.   └─parallel::parLapply(cl, data$Read.Seq, find_barcode)
 3.     ├─base::do.call(...)
 4.     └─parallel::clusterApply(...)
 5.       └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
 6.         └─parallel:::checkForRemoteErrors(val)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
one node produced an error: error in evaluating the argument 'subject' in selecting a method for function 'matchPattern': 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 ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted