Multiple platform build/check report for BioC 3.22 - BUILD results for biodbUniprot on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4883
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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*

BUILD results for biodbUniprot on nebbiolo2

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: 1.16.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbUniprot

StartedAt: 2025-12-25 16:39:21 -0500 (Thu, 25 Dec 2025)

EndedAt: 2025-12-25 16:39:33 -0500 (Thu, 25 Dec 2025)

EllapsedTime: 12.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbUniprot
###
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* checking for file ‘biodbUniprot/DESCRIPTION’ ... OK
* preparing ‘biodbUniprot’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbUniprot.Rmd’ using rmarkdown
INFO  [16:39:30.934] Loading definitions from package biodb version 1.18.0.
INFO  [16:39:32.417] Loading definitions from package biodbChebi version 1.16.0.
INFO  [16:39:32.449] Loading definitions from package biodbHmdb version 1.16.0.
INFO  [16:39:32.479] Loading definitions from package biodbNcbi version 1.14.0.
INFO  [16:39:32.502] Loading definitions from package biodbNci version 1.14.0.
INFO  [16:39:32.518] Loading definitions from package biodbUniprot version 1.16.0.
INFO  [16:39:32.638] Load 2 contents, from /home/biocbuild/.cache/R/biodb/uniprot-958d776f924f3e7a3bae586fa731b40c.

Quitting from biodbUniprot.Rmd:67-69 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/chk_error>
Error in `initialize()`:
! `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
---
Backtrace:
     ▆
  1. └─conn$getEntry(c("P01011", "P09237"))
  2.   └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  3.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  4.       └─conn$getEntryContent(ids)
  5.         └─self$getEntryContentFromDb(ch.missing.ids)
  6.           └─private$doGetEntryContentFromDb(entry.id)
  7.             └─private$doGetEntryContentOneByOne(id)
  8.               └─base::lapply(requests, fct)
  9.                 └─biodb (local) FUN(X[[i]], ...)
 10.                   └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 11.                     └─sched::Request$new(...)
 12.                       └─sched (local) initialize(...)
 13.                         └─chk::chk_true(...)
 14.                           └─chk::abort_chk(x_name, " must be TRUE", x = x)
 15.                             └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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