Back to Rapid builds (Linux only) of a subset of BioC 3.23
Report updated every 6 hours

This page was generated on 2025-11-09 10:14 -0500 (Sun, 09 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" 917
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 11/230HostnameOS / ArchINSTALLBUILDCHECK
annotate 1.89.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-11-09 06:00 -0500 (Sun, 09 Nov 2025)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: devel
git_last_commit: a7eff2c
git_last_commit_date: 2025-10-29 09:23:46 -0500 (Wed, 29 Oct 2025)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for annotate on teran2

To the developers/maintainers of the annotate package:
- 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: annotate
Version: 1.89.0
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotate
StartedAt: 2025-11-09 06:29:36 -0500 (Sun, 09 Nov 2025)
EndedAt: 2025-11-09 06:30:23 -0500 (Sun, 09 Nov 2025)
EllapsedTime: 47.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘annotate/DESCRIPTION’ ... OK
* preparing ‘annotate’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘chromLOC.Rmd’ using rmarkdown
--- finished re-building ‘chromLOC.Rmd’

--- re-building ‘useDataPkgs.Rmd’ using rmarkdown
--- finished re-building ‘useDataPkgs.Rmd’

--- re-building ‘GOusage.Rnw’ using Sweave

Attaching package: ‘graph’

The following object is masked from ‘package:XML’:

    addNode


Attaching package: ‘Rgraphviz’

The following object is masked from ‘package:annotate’:

    toFile

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

    from, to

The following objects are masked from ‘package:S4Vectors’:

    from, to

--- finished re-building ‘GOusage.Rnw’

--- re-building ‘annotate.Rnw’ using Sweave
--- finished re-building ‘annotate.Rnw’

--- re-building ‘prettyOutput.Rnw’ using Sweave
--- finished re-building ‘prettyOutput.Rnw’

--- re-building ‘query.Rnw’ using Sweave
Read 4 items

Error: processing vignette 'query.Rnw' failed with diagnostics:
 chunk 6 
Error in file(file, "r") : 
  cannot open the connection to 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=gene&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062'

--- failed re-building ‘query.Rnw’

--- re-building ‘useProbeInfo.Rnw’ using Sweave
Loading required package: org.Rn.eg.db


Loading required package: XVector
Loading required package: Seqinfo

Attaching package: ‘Biostrings’

The following object is masked from ‘package:graph’:

    complement

The following object is masked from ‘package:base’:

    strsplit


Error: processing vignette 'useProbeInfo.Rnw' failed with diagnostics:
 chunk 4 (label = getRev) 
Error in file(con, "r") : 
  cannot open the connection to 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&id=AI406693'

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

SUMMARY: processing the following files failed:
  ‘query.Rnw’ ‘useProbeInfo.Rnw’

Error: Vignette re-building failed.
In addition: Warning messages:
1: In file(file, "r") :
  cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=gene&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062': HTTP status was '400 Bad Request'
2: In file(con, "r") :
  cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&id=AI406693': HTTP status was '400 Bad Request'
Execution halted