Multiple platform build/check report for BioC 3.21 - BUILD results for biodb on nebbiolo1

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"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4581
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 biodb on nebbiolo1

To the developers/maintainers of the biodb package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodb.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: biodb

Version: 1.16.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodb

StartedAt: 2025-09-24 16:27:12 -0400 (Wed, 24 Sep 2025)

EndedAt: 2025-09-24 16:29:33 -0400 (Wed, 24 Sep 2025)

EllapsedTime: 141.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodb
###
##############################################################################
##############################################################################


* checking for file ‘biodb/DESCRIPTION’ ... OK
* preparing ‘biodb’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodb.Rmd’ using rmarkdown
INFO  [16:28:11.132] Loading definitions from package biodb version 1.16.0.
INFO  [16:28:11.598] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/chebi_extract.tsv".
INFO  [16:28:13.025] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/massbank_extract_lcms_3.tsv".
INFO  [16:28:13.773] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/massbank_extract_msms.tsv".
INFO  [16:28:14.088] Closing BiodbMain instance...
INFO  [16:28:14.090] Connector "comp.csv.file" deleted.
INFO  [16:28:14.091] Connector "mass.csv.file" deleted.
INFO  [16:28:14.093] Connector "mass.csv.file.1" deleted.
--- finished re-building ‘biodb.Rmd’

--- re-building ‘details.Rmd’ using rmarkdown
INFO  [16:28:15.491] Loading definitions from package biodb version 1.16.0.
INFO  [16:28:15.600] Closing BiodbMain instance...
INFO  [16:28:15.622] Loading definitions from package biodb version 1.16.0.
INFO  [16:28:15.852] Enable offline.
INFO  [16:28:15.855] Disable offline.
INFO  [16:28:15.981] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/chebi_extract.tsv".
INFO  [16:28:16.122] Connector "comp.csv.file" deleted.
INFO  [16:28:16.167] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/chebi_extract_custom.csv".
WARN  [16:28:16.169] Column "ID" does not match any biodb field.
WARN  [16:28:16.173] Column "molmass" does not match any biodb field.
WARN  [16:28:16.174] Column "kegg" does not match any biodb field.
INFO  [16:28:16.223] Connector "comp.csv.file" deleted.
INFO  [16:28:16.229] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/chebi_extract_custom.csv".
INFO  [16:28:16.771] Erasing all files in "/home/biocbuild/.cache/R/biodb/chebi.ex-0c5076ac2a43d16dbce503a44b09f649".
INFO  [16:28:16.814] 12 entries have been processed.
INFO  [16:28:16.928] hello
INFO  [16:28:16.947] Closing BiodbMain instance...
INFO  [16:28:16.949] Connector "comp.csv.file" deleted.
INFO  [16:28:16.950] Connector "chebi.ex" deleted.
--- finished re-building ‘details.Rmd’

--- re-building ‘entries.Rmd’ using rmarkdown
INFO  [16:28:18.118] Loading definitions from package biodb version 1.16.0.
INFO  [16:28:18.262] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/chebi_extract.tsv".
INFO  [16:28:19.553] Create cache folder "/home/biocbuild/.cache/R/biodb/comp.csv.file-fcd0ee04cf7e501ba4c32c5f88145b6c" for "comp.csv.file-fcd0ee04cf7e501ba4c32c5f88145b6c".
INFO  [16:28:19.574] Erasing all files in "/home/biocbuild/.cache/R/biodb/comp.csv.file-fcd0ee04cf7e501ba4c32c5f88145b6c".
INFO  [16:28:21.379] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/uniprot_extract.tsv".
INFO  [16:28:21.487] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/expasy_enzyme_extract.tsv".
INFO  [16:28:22.244] Creating empty database.
INFO  [16:28:22.508] Write all entries into "/tmp/RtmpW1wEgO/biodb_merged_entries_new_db8436e637a1814.tsv".
INFO  [16:28:23.046] Closing BiodbMain instance...
INFO  [16:28:23.047] Connector "comp.csv.file" deleted.
INFO  [16:28:23.049] Connector "mass.sqlite" deleted.
INFO  [16:28:23.050] Connector "comp.sqlite" deleted.
INFO  [16:28:23.051] Connector "comp.csv.file.1" deleted.
INFO  [16:28:23.053] Connector "comp.csv.file.2" deleted.
INFO  [16:28:23.054] Connector "comp.csv.file.3" deleted.
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
pandoc-citeproc: reference H not found
--- finished re-building ‘entries.Rmd’

--- re-building ‘new_connector.Rmd’ using rmarkdown
INFO  [16:28:24.944] Loading definitions from package biodb version 1.16.0.
INFO  [16:28:25.106] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi.ex-0c5076ac2a43d16dbce503a44b09f649" for "chebi.ex-0c5076ac2a43d16dbce503a44b09f649".
INFO  [16:28:26.252] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:28:27.402] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:28:28.516] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:28:30.170] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:28:33.946] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:29:06.568] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:29:07.582] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:29:08.280] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:29:09.136] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...
INFO  [16:29:09.898] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17001". Retrying connection to server...

Quitting from new_connector.Rmd:419-422 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! attempt to apply non-function
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'new_connector.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘new_connector.Rmd’

--- re-building ‘new_entry_field.Rmd’ using rmarkdown
INFO  [16:29:10.092] Loading definitions from package biodb version 1.16.0.
INFO  [16:29:11.167] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:12.049] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:12.906] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:13.828] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:14.591] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:15.442] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:16.288] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:17.135] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:17.986] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:18.759] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=40304". Retrying connection to server...
INFO  [16:29:19.609] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:20.379] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:21.152] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:22.014] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:23.298] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:24.211] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:24.978] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:26.484] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:27.375] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:29.475] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64679". Retrying connection to server...
INFO  [16:29:29.745] Connector "chebi.ex" deleted.
INFO  [16:29:29.946] Loading file database "/tmp/RtmpGMjjl2/Rinst831204fe198f2/biodb/extdata/chebi_extract_with_unknown_column.tsv".
WARN  [16:29:29.949] Column "elecCharge" does not match any biodb field.
INFO  [16:29:31.367] Connector "chebi.ex" deleted.
INFO  [16:29:31.452] Closing BiodbMain instance...
INFO  [16:29:31.453] Connector "comp.csv.file" deleted.
INFO  [16:29:31.455] Connector "chebi.ex" deleted.
--- finished re-building ‘new_entry_field.Rmd’

SUMMARY: processing the following file failed:
  ‘new_connector.Rmd’

Error: Vignette re-building failed.
Execution halted