Multiple platform build/check report for BioC 3.21 - BUILD results for biodbHmdb 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
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 biodbHmdb on palomino7

To the developers/maintainers of the biodbHmdb package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.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: biodbHmdb

Version: 1.14.0

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

StartedAt: 2025-04-21 17:45:11 -0400 (Mon, 21 Apr 2025)

EndedAt: 2025-04-21 17:46:09 -0400 (Mon, 21 Apr 2025)

EllapsedTime: 57.7 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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


* checking for file 'biodbHmdb/DESCRIPTION' ... OK
* preparing 'biodbHmdb':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'biodbHmdb.Rmd' using rmarkdown

Quitting from biodbHmdb.Rmd:76-78 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─conn$getNbEntries()
 2.   └─private$doGetNbEntries(count = count)
 3.     └─self$getEntryIds()
 4.       └─private$doGetEntryIds(max.results = max.results, ...)
 5.         └─self$download()
 6.           └─cch$setMarker(self$getCacheId(), name = "downloaded")
 7.             └─base::writeChar("", emptyFile)
 8.               └─base::file(con, "wb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted