Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).
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 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.6.6 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 |
Package 208/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbNcbi 1.12.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbNcbi |
StartedAt: 2025-10-09 17:24:24 -0400 (Thu, 09 Oct 2025) |
EndedAt: 2025-10-09 17:25:06 -0400 (Thu, 09 Oct 2025) |
EllapsedTime: 41.2 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbNcbi ### ############################################################################## ############################################################################## * 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 [17:24:59.030] Loading definitions from package biodb version 1.16.1. INFO [17:25:03.472] Loading definitions from package biodbChebi version 1.14.0. INFO [17:25:03.558] Loading definitions from package biodbHmdb version 1.14.0. INFO [17:25:03.652] Loading definitions from package biodbNcbi version 1.12.0. INFO [17:25:03.721] Loading definitions from package biodbNci version 1.12.0. INFO [17:25:03.741] Loading definitions from package biodbUniprot version 1.14.0. 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