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This page was generated on 2025-10-23 11:30 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 3809
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 213/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbUniprot 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-22 15:48 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbUniprot
git_branch: devel
git_last_commit: 54ad981
git_last_commit_date: 2025-07-24 10:48:06 -0400 (Thu, 24 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for biodbUniprot on nebbiolo1

To the developers/maintainers of the biodbUniprot package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbUniprot.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: biodbUniprot
Version: 1.15.1
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodbUniprot
StartedAt: 2025-10-22 22:11:18 -0000 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 22:11:29 -0000 (Wed, 22 Oct 2025)
EllapsedTime: 11.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodbUniprot
###
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* checking for file ‘biodbUniprot/DESCRIPTION’ ... OK
* preparing ‘biodbUniprot’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘biodbUniprot.Rmd’ using rmarkdown
INFO  [22:11:27.378] Loading definitions from package biodb version 1.17.2.
INFO  [22:11:28.660] Loading definitions from package biodbChebi version 1.15.1.
INFO  [22:11:28.690] Loading definitions from package biodbHmdb version 1.15.1.
INFO  [22:11:28.721] Loading definitions from package biodbNcbi version 1.13.1.
INFO  [22:11:28.744] Loading definitions from package biodbNci version 1.13.1.
INFO  [22:11:28.751] Loading definitions from package biodbUniprot version 1.15.1.
INFO  [22:11:28.865] Load 2 contents, from /home/biocbuild/.cache/R/biodb/uniprot-958d776f924f3e7a3bae586fa731b40c.

Quitting from biodbUniprot.Rmd:67-69 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbUniprot.Rmd' failed with diagnostics:
`chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
--- failed re-building ‘biodbUniprot.Rmd’

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

Error: Vignette re-building failed.
Execution halted