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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
###
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* checking for file ‘recountWorkflow/DESCRIPTION’ ... OK
* preparing ‘recountWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘recount-workflow.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
Content type 'binary/octet-stream' length 12604886 bytes (12.0 MB)
==================================================
downloaded 12.0 MB

trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true'
Content type 'application/octet-stream' length 548129 bytes (535 KB)
==================================================
downloaded 535 KB

[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'gene_report.knit'

Quitting from recount-workflow.Rmd:592-610 [goanalysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. └─clusterProfiler::enrichGO(...)
  2.   └─clusterProfiler::enrichGO(...)
  3.     └─clusterProfiler:::get_GO_data(OrgDb, ont, keyType)
  4.       ├─base::suppressMessages(...)
  5.       │ └─base::withCallingHandlers(...)
  6.       ├─AnnotationDbi::mapIds(...)
  7.       └─AnnotationDbi::mapIds(...)
  8.         └─AnnotationDbi::mapIds_base(x, keys, column, keytype, ..., multiVals = multiVals)
  9.           ├─AnnotationDbi::select(...)
 10.           └─AnnotationDbi::select(...)
 11.             └─AnnotationDbi:::.select(...)
 12.               └─AnnotationDbi::testSelectArgs(...)
 13.                 └─AnnotationDbi:::.testForValidKeys(x, keys, keytype, fks)
 14.                   ├─AnnotationDbi::keys(x, keytype)
 15.                   └─AnnotationDbi::keys(x, keytype)
 16.                     └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 17.                       └─AnnotationDbi:::.keys(x, keytype)
 18.                         └─AnnotationDbi:::.legacyKeys(x, keytype)
 19.                           └─AnnotationDbi:::.queryForKeys(x, keytype)
 20.                             └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 21.                               ├─DBI::dbGetQuery(conn, SQL)
 22.                               └─DBI::dbGetQuery(conn, SQL)
 23.                                 └─DBI (local) .local(conn, statement, ...)
 24.                                   ├─DBI::dbSendQuery(conn, statement, ...)
 25.                                   └─RSQLite::dbSendQuery(conn, statement, ...)
 26.                                     └─RSQLite (local) .local(conn, statement, ...)
 27.                                       ├─methods::new(...)
 28.                                       │ ├─methods::initialize(value, ...)
 29.                                       │ └─methods::initialize(value, ...)
 30.                                       └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following file failed:
  ‘recount-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted