| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-11-01 12:02 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 | ||||
| Package 212/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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To the developers/maintainers of the biodbNcbi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbNcbi.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. |
| Package: biodbNcbi |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbNcbi |
| StartedAt: 2025-10-31 16:40:59 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 16:41:14 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 15.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbNcbi
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* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* preparing ‘biodbNcbi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbNcbi.Rmd’ using rmarkdown
INFO [16:41:11.475] Loading definitions from package biodb version 1.18.0.
INFO [16:41:12.926] Loading definitions from package biodbChebi version 1.16.0.
INFO [16:41:12.957] Loading definitions from package biodbHmdb version 1.16.0.
INFO [16:41:12.988] Loading definitions from package biodbNcbi version 1.14.0.
INFO [16:41:13.021] Loading definitions from package biodbNci version 1.14.0.
INFO [16:41:13.028] Loading definitions from package biodbUniprot version 1.16.0.
Quitting from biodbNcbi.Rmd:72-74 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! 'BiodbUrl' is not an exported object from 'namespace:biodb'
---
Backtrace:
▆
1. └─gene$getNbEntries()
2. └─private$doGetNbEntries(count = count)
3. └─self$wsEinfo(retfmt = "parsed")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'biodbNcbi.Rmd' failed with diagnostics:
'BiodbUrl' is not an exported object from 'namespace:biodb'
--- failed re-building ‘biodbNcbi.Rmd’
SUMMARY: processing the following file failed:
‘biodbNcbi.Rmd’
Error: Vignette re-building failed.
Execution halted