Build/check report for BioC 3.24 - BUILD results for VISTA on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4844
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BUILD results for VISTA on nebbiolo2

To the developers/maintainers of the VISTA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VISTA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: VISTA

Version: 1.1.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 VISTA

StartedAt: 2026-05-04 20:47:40 -0400 (Mon, 04 May 2026)

EndedAt: 2026-05-04 20:50:14 -0400 (Mon, 04 May 2026)

EllapsedTime: 154.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 VISTA
###
##############################################################################
##############################################################################


* checking for file ‘VISTA/DESCRIPTION’ ... OK
* preparing ‘VISTA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘VISTA-airway.Rmd’ using rmarkdown
Registered S3 methods overwritten by 'ggpp':
  method                  from   
  heightDetails.titleGrob ggplot2
  widthDetails.titleGrob  ggplot2

Quitting from VISTA-airway.Rmd:1153-1166 [go-bp]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. └─VISTA::get_go_enrichment(...)
  2.   └─clusterProfiler::enrichGO(...)
  3.     └─clusterProfiler::enrichGO(...)
  4.       └─clusterProfiler:::get_GO_data(OrgDb, ont, keyType)
  5.         ├─base::suppressMessages(...)
  6.         │ └─base::withCallingHandlers(...)
  7.         ├─AnnotationDbi::mapIds(...)
  8.         └─AnnotationDbi::mapIds(...)
  9.           └─AnnotationDbi::mapIds_base(x, keys, column, keytype, ..., multiVals = multiVals)
 10.             ├─AnnotationDbi::select(...)
 11.             └─AnnotationDbi::select(...)
 12.               └─AnnotationDbi:::.select(...)
 13.                 └─AnnotationDbi::testSelectArgs(...)
 14.                   └─AnnotationDbi:::.testForValidKeys(x, keys, keytype, fks)
 15.                     ├─AnnotationDbi::keys(x, keytype)
 16.                     └─AnnotationDbi::keys(x, keytype)
 17.                       └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 18.                         └─AnnotationDbi:::.keys(x, keytype)
 19.                           └─AnnotationDbi:::.legacyKeys(x, keytype)
 20.                             └─AnnotationDbi:::.queryForKeys(x, keytype)
 21.                               └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 22.                                 ├─DBI::dbGetQuery(conn, SQL)
 23.                                 └─DBI::dbGetQuery(conn, SQL)
 24.                                   └─DBI (local) .local(conn, statement, ...)
 25.                                     ├─DBI::dbSendQuery(conn, statement, ...)
 26.                                     └─RSQLite::dbSendQuery(conn, statement, ...)
 27.                                       └─RSQLite (local) .local(conn, statement, ...)
 28.                                         ├─methods::new(...)
 29.                                         │ ├─methods::initialize(value, ...)
 30.                                         │ └─methods::initialize(value, ...)
 31.                                         └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following file failed:
  ‘VISTA-airway.Rmd’

Error: Vignette re-building failed.
Execution halted