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This page was generated on 2026-02-05 11:32 -0500 (Thu, 05 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" 4852
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 862/2347HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOmetadb 1.73.0  (landing page)
Jack Zhu
Snapshot Date: 2026-02-04 13:40 -0500 (Wed, 04 Feb 2026)
git_url: https://git.bioconductor.org/packages/GEOmetadb
git_branch: devel
git_last_commit: c3ec251
git_last_commit_date: 2025-10-29 10:00:25 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
See other builds for GEOmetadb in R Universe.

BUILD results for GEOmetadb on nebbiolo1

To the developers/maintainers of the GEOmetadb package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOmetadb.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: GEOmetadb
Version: 1.73.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GEOmetadb
StartedAt: 2026-02-04 17:49:12 -0500 (Wed, 04 Feb 2026)
EndedAt: 2026-02-04 17:49:26 -0500 (Wed, 04 Feb 2026)
EllapsedTime: 14.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GEOmetadb
###
##############################################################################
##############################################################################


* checking for file ‘GEOmetadb/DESCRIPTION’ ... OK
* preparing ‘GEOmetadb’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GEOmetadb.Rmd’ using rmarkdown
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz'
Content type 'application/x-gzip' length 20889492 bytes (19.9 MB)
==================================================
downloaded 19.9 MB


Quitting from GEOmetadb.Rmd:283-288 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! `src_sqlite()` was deprecated in dplyr 1.0.0
  and is now defunct.
ℹ Please use `tbl()` directly with a database
  connection
---
Backtrace:
    ▆
 1. └─dplyr::src_sqlite(demo_sqlfile)
 2.   └─lifecycle::deprecate_stop("1.0.0", "src_sqlite()", details = "Please use `tbl()` directly with a database connection")
 3.     └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GEOmetadb.Rmd' failed with diagnostics:
`src_sqlite()` was deprecated in dplyr 1.0.0
and is now defunct.
ℹ Please use `tbl()` directly with a database
  connection
--- failed re-building ‘GEOmetadb.Rmd’

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

Error: Vignette re-building failed.
Execution halted