Multiple platform build/check report for BioC 3.21 - BUILD results for biodbNci on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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 kjohnson1

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: 1.12.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbNci

StartedAt: 2025-10-13 20:04:40 -0400 (Mon, 13 Oct 2025)

EndedAt: 2025-10-13 20:05:15 -0400 (Mon, 13 Oct 2025)

EllapsedTime: 34.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data 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  [20:05:11.187] Loading definitions from package biodb version 1.16.1.
INFO  [20:05:13.321] Loading definitions from package biodbChebi version 1.14.0.
INFO  [20:05:13.354] Loading definitions from package biodbHmdb version 1.14.0.
INFO  [20:05:13.388] Loading definitions from package biodbNcbi version 1.12.0.
INFO  [20:05:13.414] Loading definitions from package biodbNci version 1.12.0.
INFO  [20:05:13.424] Loading definitions from package biodbUniprot version 1.14.0.
INFO  [20:05:13.793] Extract whole database of nci.cactus.
INFO  [20:05:13.795] 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