Multiple platform build/check report for BioC 3.21 - BUILD results for biodbUniprot on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
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 palomino7

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: 1.14.0

Command: chmod a+r biodbUniprot -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data biodbUniprot

StartedAt: 2025-04-22 17:50:03 -0400 (Tue, 22 Apr 2025)

EndedAt: 2025-04-22 17:50:29 -0400 (Tue, 22 Apr 2025)

EllapsedTime: 26.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r biodbUniprot -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data biodbUniprot
###
##############################################################################
##############################################################################


* 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

Quitting from biodbUniprot.Rmd:67-69 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
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$doGetEntryContentOneByOne(id)
  8.               └─scheduler$sendRequest(requests[[i]])
  9.                 └─cch$saveContentToFile(...)
 10.                   └─private$doSaveContentToFile(...)
 11.                     └─biodb:::saveContentsToFiles(file.paths, content)
 12.                       └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 13.                         └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 14.                           └─base::cat(cnt, file = f)
 15.                             └─base::file(file, ifelse(append, "a", "w"))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbUniprot.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'biodbUniprot.Rmd'

SUMMARY: processing the following file failed:
  'biodbUniprot.Rmd'

Error: Vignette re-building failed.
Execution halted