| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-06 11:35 -0500 (Tue, 06 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 210/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.17.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | 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: 1.17.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi |
| StartedAt: 2026-01-05 15:45:24 -0500 (Mon, 05 Jan 2026) |
| EndedAt: 2026-01-05 15:45:50 -0500 (Mon, 05 Jan 2026) |
| EllapsedTime: 26.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘biodbChebi.Rmd’ using rmarkdown
INFO [15:45:28.367] Loading definitions from package biodb version 1.19.0.
INFO [15:45:29.142] Loading definitions from package biodbChebi version 1.17.0.
INFO [15:45:29.286] Load 3 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
INFO [15:45:29.294] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/sched.
INFO [15:45:30.215] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:31.327] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:31.992] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:32.661] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:33.332] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:34.005] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:34.668] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:35.334] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:36.006] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:36.671] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
INFO [15:45:36.687] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/sched.
INFO [15:45:37.357] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:38.273] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:38.943] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:39.620] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:40.288] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:40.953] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:41.629] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:42.293] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:42.960] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:43.624] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17053". Retrying connection to server...
INFO [15:45:43.625] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/sched.
INFO [15:45:44.292] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:44.964] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:45.627] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:46.294] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:46.971] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:47.646] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:48.311] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:48.974] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:49.638] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:50.304] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
INFO [15:45:50.305] Save 3 contents to /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
Quitting from biodbChebi.Rmd:72-74 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! attempt to apply non-function
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'biodbChebi.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘biodbChebi.Rmd’
SUMMARY: processing the following file failed:
‘biodbChebi.Rmd’
Error: Vignette re-building failed.
Execution halted