| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-02 11:37 -0400 (Thu, 02 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" | 4831 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
| 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 206/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.14.0 (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 biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.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: biodbChebi |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi |
| StartedAt: 2025-10-01 16:29:40 -0400 (Wed, 01 Oct 2025) |
| EndedAt: 2025-10-01 16:29:52 -0400 (Wed, 01 Oct 2025) |
| EllapsedTime: 12.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi
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* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* preparing ‘biodbChebi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbChebi.Rmd’ using rmarkdown
INFO [16:29:48.901] Loading definitions from package biodb version 1.16.1.
INFO [16:29:50.422] Loading definitions from package biodbChebi version 1.14.0.
INFO [16:29:50.452] Loading definitions from package biodbHmdb version 1.14.0.
INFO [16:29:50.484] Loading definitions from package biodbNcbi version 1.12.0.
INFO [16:29:50.517] Loading definitions from package biodbNci version 1.12.0.
INFO [16:29:50.524] Loading definitions from package biodbUniprot version 1.14.0.
INFO [16:29:50.636] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
Quitting from biodbChebi.Rmd:94-96 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `self$wsWsdl()`:
! object 'BiodbUrl' not found
---
Backtrace:
▆
1. └─chebi$searchCompound(name = "aspartic", max.results = 3)
2. └─self$searchForEntries(list(name = name), max.results = max.results)
3. └─private$doSearchForEntries(fields = fields, max.results = max.results)
4. └─self$wsGetLiteEntity(...)
5. ├─chk::chk_subset(search.category, self$getSearchCategories())
6. │ └─chk::vld_subset(x, values)
7. │ └─x %in% values
8. └─self$getSearchCategories()
9. └─self$getWsdlEnumeration("SearchCategory")
10. ├─XML::xpathSApply(...)
11. │ └─XML::xpathApply(...)
12. └─self$getWsdl()
13. └─self$wsWsdl(retfmt = "parsed")
14. └─self$makeRequest(...)
15. └─sched::Request$new(...)
16. └─sched (local) initialize(...)
17. └─chk::chk_is(url, "URL")
18. └─chk::vld_is(x, class)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'biodbChebi.Rmd' failed with diagnostics:
object 'BiodbUrl' not found
--- failed re-building ‘biodbChebi.Rmd’
SUMMARY: processing the following file failed:
‘biodbChebi.Rmd’
Error: Vignette re-building failed.
Execution halted