Build/check report for BioC 3.22 - BUILD results for biodbChebi on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4891
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 nebbiolo2

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: 1.16.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbChebi

StartedAt: 2026-02-25 16:34:40 -0500 (Wed, 25 Feb 2026)

EndedAt: 2026-02-25 16:35:17 -0500 (Wed, 25 Feb 2026)

EllapsedTime: 37.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbChebi
###
##############################################################################
##############################################################################


* 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  [16:34:48.821] Loading definitions from package biodb version 1.18.0.
INFO  [16:34:50.303] Loading definitions from package biodbChebi version 1.16.0.
INFO  [16:34:50.334] Loading definitions from package biodbHmdb version 1.16.0.
INFO  [16:34:50.365] Loading definitions from package biodbNcbi version 1.14.0.
INFO  [16:34:50.388] Loading definitions from package biodbNci version 1.14.0.
INFO  [16:34:50.404] Loading definitions from package biodbUniprot version 1.16.0.
INFO  [16:34:50.519] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
INFO  [16:34:50.537] Load 1 contents, from /home/biocbuild/.cache/R/sched.
INFO  [16:34:51.593] 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  [16:34:52.770] 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  [16:34:53.691] 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  [16:34:54.543] 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  [16:34:55.304] 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  [16:34:56.123] 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  [16:34:56.936] 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  [16:34:57.684] 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  [16:34:58.461] 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  [16:34:59.338] 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  [16:34:59.391] Load 1 contents, from /home/biocbuild/.cache/R/sched.
INFO  [16:35:00.206] 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  [16:35:01.031] 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  [16:35:01.829] 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  [16:35:02.675] 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  [16:35:03.479] 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  [16:35:04.291] 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  [16:35:05.096] 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  [16:35:05.854] 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  [16:35:06.629] 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  [16:35:07.432] 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  [16:35:07.443] Load 1 contents, from /home/biocbuild/.cache/R/sched.
INFO  [16:35:08.280] 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  [16:35:09.031] 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  [16:35:10.776] 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  [16:35:11.560] 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  [16:35:12.488] 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  [16:35:13.262] 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  [16:35:13.940] 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  [16:35:14.743] 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  [16:35:15.485] 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  [16:35:16.312] 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  [16:35:16.317] 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