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###
### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotation
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* checking for file ‘annotation/DESCRIPTION’ ... OK
* preparing ‘annotation’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Annotating_Genomic_Ranges.Rmd’ using rmarkdown

Quitting from Annotating_Genomic_Ranges.Rmd:157-162 [unnamed-chunk-15]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. ├─VariantAnnotation::locateVariants(gr_hg19, txdb_hg19, AllVariants())
  2. └─VariantAnnotation::locateVariants(gr_hg19, txdb_hg19, AllVariants())
  3.   └─VariantAnnotation (local) .local(query, subject, region, ...)
  4.     ├─VariantAnnotation::locateVariants(...)
  5.     └─VariantAnnotation::locateVariants(...)
  6.       └─VariantAnnotation (local) .local(query, subject, region, ...)
  7.         ├─AnnotationDbi::select(...)
  8.         └─GenomicFeatures (local) select(subject, as.character(res$TXID), "GENEID", "TXID")
  9.           └─GenomicFeatures:::.select(x, keys, columns, keytype, ...)
 10.             └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 11.               ├─DBI::dbGetQuery(conn, SQL)
 12.               └─DBI::dbGetQuery(conn, SQL)
 13.                 └─DBI (local) .local(conn, statement, ...)
 14.                   ├─DBI::dbSendQuery(conn, statement, ...)
 15.                   └─RSQLite::dbSendQuery(conn, statement, ...)
 16.                     └─RSQLite (local) .local(conn, statement, ...)
 17.                       ├─methods::new(...)
 18.                       │ ├─methods::initialize(value, ...)
 19.                       │ └─methods::initialize(value, ...)
 20.                       └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Annotating_Genomic_Ranges.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘Annotating_Genomic_Ranges.Rmd’

--- re-building ‘Annotation_Resources.Rmd’ using rmarkdown

Quitting from Annotation_Resources.Rmd:242-245 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. ├─base::subset(ah, ah$rdataclass == "OrgDb")
  2. └─AnnotationHub::subset(ah, ah$rdataclass == "OrgDb")
  3.   └─AnnotationHub (local) .local(x, ...)
  4.     ├─S4Vectors::mcols(x)
  5.     └─AnnotationHub::mcols(x)
  6.       └─AnnotationHub (local) .local(x, ...)
  7.         ├─S4Vectors::DataFrame(.resource_table(x))
  8.         └─AnnotationHub:::.resource_table(x)
  9.           ├─S4Vectors::I(.collapse_as_list(x, .tags))
 10.           └─AnnotationHub:::.collapse_as_list(x, .tags)
 11.             └─AnnotationHub (local) FUN(x)
 12.               └─AnnotationHub:::.db_query(dbfile(x), query)
 13.                 ├─DBI::dbGetQuery(path, query)
 14.                 └─DBI::dbGetQuery(path, query)
 15.                   └─DBI (local) .local(conn, statement, ...)
 16.                     ├─DBI::dbFetch(rs, n = n, ...)
 17.                     └─RSQLite::dbFetch(rs, n = n, ...)
 18.                       └─RSQLite (local) .local(res, n, ...)
 19.                         └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Annotation_Resources.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘Annotation_Resources.Rmd’

SUMMARY: processing the following files failed:
  ‘Annotating_Genomic_Ranges.Rmd’ ‘Annotation_Resources.Rmd’

Error: Vignette re-building failed.
Execution halted