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

To the developers/maintainers of the scGPS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scGPS.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: scGPS

Version: 1.27.0

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

StartedAt: 2026-05-04 19:58:14 -0400 (Mon, 04 May 2026)

EndedAt: 2026-05-04 20:02:29 -0400 (Mon, 04 May 2026)

EllapsedTime: 254.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 scGPS
###
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* checking for file ‘scGPS/DESCRIPTION’ ... OK
* preparing ‘scGPS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from vignette.Rmd:215-254 [find_markers]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. └─scGPS::annotate_clusters(genes, pvalueCutoff = 0.05, gene_symbol = TRUE)
  2.   └─clusterProfiler::bitr(...)
  3.     ├─base::suppressWarnings(...)
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─AnnotationDbi::select(...)
  6.     └─AnnotationDbi::select(...)
  7.       └─AnnotationDbi:::.select(...)
  8.         └─AnnotationDbi::testSelectArgs(...)
  9.           └─AnnotationDbi:::.testForValidKeys(x, keys, keytype, fks)
 10.             ├─AnnotationDbi::keys(x, keytype)
 11.             └─AnnotationDbi::keys(x, keytype)
 12.               └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 13.                 └─AnnotationDbi:::.keys(x, keytype)
 14.                   └─AnnotationDbi:::.legacyKeys(x, keytype)
 15.                     └─AnnotationDbi:::.queryForKeys(x, keytype)
 16.                       └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 17.                         ├─DBI::dbGetQuery(conn, SQL)
 18.                         └─DBI::dbGetQuery(conn, SQL)
 19.                           └─DBI (local) .local(conn, statement, ...)
 20.                             ├─DBI::dbFetch(rs, n = n, ...)
 21.                             └─RSQLite::dbFetch(rs, n = n, ...)
 22.                               └─RSQLite (local) .local(res, n, ...)
 23.                                 └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted