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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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 biodbNci on nebbiolo2

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

Version: 1.13.1

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

StartedAt: 2025-08-08 16:19:06 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 16:19:38 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 32.0 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 biodbNci
###
##############################################################################
##############################################################################


* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* preparing ‘biodbNci’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbNci.Rmd’ using rmarkdown
INFO  [16:19:35.930] Loading definitions from package biodb version 1.17.1.
INFO  [16:19:37.403] Loading definitions from package biodbChebi version 1.15.1.
INFO  [16:19:37.434] Loading definitions from package biodbHmdb version 1.15.1.
INFO  [16:19:37.464] Loading definitions from package biodbNcbi version 1.13.1.
INFO  [16:19:37.487] Loading definitions from package biodbNci version 1.13.1.
INFO  [16:19:37.494] Loading definitions from package biodbUniprot version 1.15.1.
INFO  [16:19:37.661] Extract whole database of nci.cactus.
INFO  [16:19:37.662] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....

Quitting from biodbNci.Rmd:72-75 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `private$doExtractDownload()`:
! attempt to apply non-function
---
Backtrace:
    ▆
 1. └─conn$getEntryIds(2)
 2.   └─private$doGetEntryIds(max.results = max.results, ...)
 3.     └─self$download()
 4.       └─private$doExtractDownload()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbNci.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘biodbNci.Rmd’

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

Error: Vignette re-building failed.
Execution halted