Multiple platform build/check report for BioC 3.23 - BUILD results for biodbChebi on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4928
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4659
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 biodbChebi on nebbiolo1

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.

raw results

Summary

Package: biodbChebi

Version: 1.17.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi

StartedAt: 2026-04-15 16:39:25 -0400 (Wed, 15 Apr 2026)

EndedAt: 2026-04-15 16:40:01 -0400 (Wed, 15 Apr 2026)

EllapsedTime: 36.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘biodbChebi.Rmd’ using rmarkdown
INFO  [16:39:34.419] Loading definitions from package biodb version 1.19.0.
INFO  [16:39:35.845] Loading definitions from package biodbChebi version 1.17.1.
INFO  [16:39:36.002] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
INFO  [16:39:36.020] Load 1 contents, from /home/biocbuild/.cache/R/sched.
INFO  [16:39:37.362] 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  [16:39:38.145] 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  [16:39:38.927] 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  [16:39:39.707] 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  [16:39:40.493] 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  [16:39:41.268] 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  [16:39:42.070] 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  [16:39:42.864] 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  [16:39:43.649] 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  [16:39:44.435] 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  [16:39:44.528] Load 1 contents, from /home/biocbuild/.cache/R/sched.
INFO  [16:39:45.422] 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  [16:39:46.204] 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  [16:39:47.002] 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  [16:39:47.795] 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  [16:39:48.515] 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  [16:39:49.387] 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  [16:39:50.164] 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  [16:39:50.944] 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  [16:39:51.955] 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  [16:39:52.734] 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  [16:39:52.739] Load 1 contents, from /home/biocbuild/.cache/R/sched.
INFO  [16:39:53.534] 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  [16:39:54.330] 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  [16:39:55.204] 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  [16:39:55.984] 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  [16:39:56.766] 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  [16:39:57.606] 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  [16:39:58.405] 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  [16:39:59.184] 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  [16:39:59.977] 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  [16:40:00.762] 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  [16:40:00.769] Save 3 contents to /home/biocbuild/.cache/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