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


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

Quitting from annotatr-vignette.Rmd:153-171 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mergeNamedAtomicVectors()`:
! sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
---
Backtrace:
     ▆
  1. └─annotatr::build_annotations(genome = "hg19", annotations = annots)
  2.   ├─methods (local) c(...)
  3.   └─S4Vectors (local) c(...)
  4.     └─S4Vectors (local) .local(x, ...)
  5.       ├─S4Vectors::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
  6.       └─IRanges::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
  7.         ├─S4Vectors::bindROWS(...)
  8.         └─GenomicRanges::bindROWS(...)
  9.           └─GenomicRanges:::combine_seqinfo_from_GenomicRanges_objects(all_objects)
 10.             ├─BiocGenerics::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
 11.             ├─base::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
 12.             ├─base (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`)
 13.             └─Seqinfo (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`)
 14.               └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
 15.                 └─Seqinfo:::.merge_two_Seqinfo_objects(x, y)
 16.                   └─Seqinfo:::mergeNamedAtomicVectors(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'annotatr-vignette.Rmd' failed with diagnostics:
sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
--- failed re-building ‘annotatr-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘annotatr-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted