Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-07-28 11:40 -0400 (Mon, 28 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 71/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.86.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-07-24 13:40 -0400 (Thu, 24 Jul 2025)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: RELEASE_3_21
git_last_commit: fc6937c
git_last_commit_date: 2025-06-18 14:09:36 -0400 (Wed, 18 Jun 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


BUILD results for annotate on nebbiolo1

To the developers/maintainers of the annotate package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotate.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: annotate
Version: 1.86.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotate
StartedAt: 2025-07-27 16:07:27 -0400 (Sun, 27 Jul 2025)
EndedAt: 2025-07-27 16:08:19 -0400 (Sun, 27 Jul 2025)
EllapsedTime: 52.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/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 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

Error: processing vignette 'query.Rnw' failed with diagnostics:
 chunk 3 (label = getabsts) 
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=PubMed&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



Error: processing vignette 'useProbeInfo.Rnw' failed with diagnostics:
 chunk 3 (label = getACC) 
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=NM_031013'

--- 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=PubMed&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062': HTTP status was '500 Internal Server Error'
2: In file(con, "r") :
  cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&id=NM_031013': HTTP status was '500 Internal Server Error'
Execution halted