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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1161/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LRBaseDbi 2.19.1  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2025-10-26 13:45 -0400 (Sun, 26 Oct 2025)
git_url: https://git.bioconductor.org/packages/LRBaseDbi
git_branch: devel
git_last_commit: 0ecd059
git_last_commit_date: 2025-05-23 09:44:00 -0400 (Fri, 23 May 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped


BUILD results for LRBaseDbi on kjohnson3

To the developers/maintainers of the LRBaseDbi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LRBaseDbi.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: LRBaseDbi
Version: 2.19.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data LRBaseDbi
StartedAt: 2025-10-26 17:01:42 -0400 (Sun, 26 Oct 2025)
EndedAt: 2025-10-26 17:07:25 -0400 (Sun, 26 Oct 2025)
EllapsedTime: 342.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data LRBaseDbi
###
##############################################################################
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* checking for file ‘LRBaseDbi/DESCRIPTION’ ... OK
* preparing ‘LRBaseDbi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘LRBaseDbi.Rnw’ using Sweave
LRBase.XXX.eg.db-type packages are deprecated since Bioconductor 3.14. Use AnnotationHub instead. For details, check the vignette of LRBaseDbi
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead
Error while performing HEAD request.
   Proceeding without cache information.
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/AnnotationHub/file15e056edd12d9’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [annotationhub.bioconductor.org]:
Connection timed out after 10003 milliseconds
Warning: bfcdownload() failed
  rid: BFC1
  file: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
  reason: download failed
Warning: Could not check database for updates.
  Database source currently unreachable.
  This should only be a temporary interruption. 
  Using previously cached version.

Error: processing vignette 'LRBaseDbi.Rnw' failed with diagnostics:
 chunk 2 
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
Connection timed out after 10003 milliseconds
  Consider rerunning with 'localHub=TRUE'

--- failed re-building ‘LRBaseDbi.Rnw’

SUMMARY: processing the following file failed:
  ‘LRBaseDbi.Rnw’

Error: Vignette re-building failed.
Execution halted