Multiple platform build/check report for BioC 3.21 - BUILD results for biodb on merida1

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 merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodb

StartedAt: 2025-09-22 17:22:13 -0400 (Mon, 22 Sep 2025)

EndedAt: 2025-09-22 17:26:13 -0400 (Mon, 22 Sep 2025)

EllapsedTime: 239.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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  [17:24:47.879] Loading definitions from package biodb version 1.16.0.
INFO  [17:24:49.369] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/chebi_extract.tsv".
INFO  [17:24:54.592] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/massbank_extract_lcms_3.tsv".
INFO  [17:24:57.207] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/massbank_extract_msms.tsv".
INFO  [17:24:58.367] Closing BiodbMain instance...
INFO  [17:24:58.370] Connector "comp.csv.file" deleted.
INFO  [17:24:58.374] Connector "mass.csv.file" deleted.
INFO  [17:24:58.377] Connector "mass.csv.file.1" deleted.
--- finished re-building ‘biodb.Rmd’

--- re-building ‘details.Rmd’ using rmarkdown
INFO  [17:25:01.880] Loading definitions from package biodb version 1.16.0.
INFO  [17:25:02.243] Closing BiodbMain instance...
INFO  [17:25:02.346] Loading definitions from package biodb version 1.16.0.
INFO  [17:25:03.330] Enable offline.
INFO  [17:25:03.335] Disable offline.
INFO  [17:25:03.940] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/chebi_extract.tsv".
INFO  [17:25:04.541] Connector "comp.csv.file" deleted.
INFO  [17:25:04.750] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/chebi_extract_custom.csv".
WARN  [17:25:04.755] Column "ID" does not match any biodb field.
WARN  [17:25:04.765] Column "molmass" does not match any biodb field.
WARN  [17:25:04.769] Column "kegg" does not match any biodb field.
INFO  [17:25:04.997] Connector "comp.csv.file" deleted.
INFO  [17:25:05.012] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/chebi_extract_custom.csv".
INFO  [17:25:07.273] Erasing all files in "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi.ex-0c5076ac2a43d16dbce503a44b09f649".
INFO  [17:25:07.470] 12 entries have been processed.
INFO  [17:25:08.056] hello
INFO  [17:25:08.155] Closing BiodbMain instance...
INFO  [17:25:08.159] Connector "comp.csv.file" deleted.
INFO  [17:25:08.162] Connector "chebi.ex" deleted.
--- finished re-building ‘details.Rmd’

--- re-building ‘entries.Rmd’ using rmarkdown
INFO  [17:25:11.131] Loading definitions from package biodb version 1.16.0.
INFO  [17:25:11.672] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/chebi_extract.tsv".
INFO  [17:25:16.818] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/comp.csv.file-1d9636e0a8a9689903116a6ce8d8ee5a" for "comp.csv.file-1d9636e0a8a9689903116a6ce8d8ee5a".
INFO  [17:25:16.914] Erasing all files in "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/comp.csv.file-1d9636e0a8a9689903116a6ce8d8ee5a".
INFO  [17:25:22.606] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/uniprot_extract.tsv".
INFO  [17:25:22.950] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/expasy_enzyme_extract.tsv".
INFO  [17:25:25.583] Creating empty database.
INFO  [17:25:26.469] Write all entries into "/tmp/RtmpO1FiwP/biodb_merged_entries_new_db4b042725ac35.tsv".
INFO  [17:25:28.399] Closing BiodbMain instance...
INFO  [17:25:28.449] Connector "comp.csv.file" deleted.
INFO  [17:25:28.453] Connector "mass.sqlite" deleted.
INFO  [17:25:28.457] Connector "comp.sqlite" deleted.
INFO  [17:25:28.460] Connector "comp.csv.file.1" deleted.
INFO  [17:25:28.466] Connector "comp.csv.file.2" deleted.
INFO  [17:25:28.469] 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  [17:25:33.869] Loading definitions from package biodb version 1.16.0.
INFO  [17:25:34.454] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi.ex-0c5076ac2a43d16dbce503a44b09f649" for "chebi.ex-0c5076ac2a43d16dbce503a44b09f649".
INFO  [17:25:35.656] 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  [17:25:36.737] 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  [17:25:37.492] 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  [17:25:38.250] 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  [17:25:39.007] 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  [17:25:40.767] 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  [17:25:41.844] 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  [17:25:42.879] 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  [17:25:43.639] 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  [17:25:44.396] 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  [17:25:44.859] Loading definitions from package biodb version 1.16.0.
INFO  [17:25:46.763] 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  [17:25:47.516] 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  [17:25:48.272] 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  [17:25:49.288] 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  [17:25:50.296] 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  [17:25:51.054] 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  [17:25:51.811] 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  [17:25:52.677] 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  [17:25:53.618] 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  [17:25:54.375] 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  [17:25:55.240] 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  [17:25:55.998] 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  [17:25:56.754] 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  [17:25:57.512] 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  [17:25:58.536] 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  [17:25:59.365] 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  [17:26:00.122] 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  [17:26:00.878] 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  [17:26:01.915] 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  [17:26:02.861] 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  [17:26:04.018] Connector "chebi.ex" deleted.
INFO  [17:26:04.900] Loading file database "/private/tmp/RtmpDmEw7f/Rinst36fc2d0d6953/biodb/extdata/chebi_extract_with_unknown_column.tsv".
WARN  [17:26:04.907] Column "elecCharge" does not match any biodb field.
INFO  [17:26:10.005] Connector "chebi.ex" deleted.
INFO  [17:26:10.368] Closing BiodbMain instance...
INFO  [17:26:10.372] Connector "comp.csv.file" deleted.
INFO  [17:26:10.375] 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