Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-09-25 11:40 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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

Package 205/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodb
git_branch: RELEASE_3_21
git_last_commit: 2dd6d33
git_last_commit_date: 2025-04-15 12:29:47 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for biodb on kjohnson1

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 20:07:59 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 20:10:49 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 170.9 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  [20:09:02.940] Loading definitions from package biodb version 1.16.0.
INFO  [20:09:03.846] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/chebi_extract.tsv".
INFO  [20:09:06.498] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/massbank_extract_lcms_3.tsv".
INFO  [20:09:07.599] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/massbank_extract_msms.tsv".
INFO  [20:09:08.214] Closing BiodbMain instance...
INFO  [20:09:08.216] Connector "comp.csv.file" deleted.
INFO  [20:09:08.218] Connector "mass.csv.file" deleted.
INFO  [20:09:08.219] Connector "mass.csv.file.1" deleted.
--- finished re-building ‘biodb.Rmd’

--- re-building ‘details.Rmd’ using rmarkdown
INFO  [20:09:10.207] Loading definitions from package biodb version 1.16.0.
INFO  [20:09:10.396] Closing BiodbMain instance...
INFO  [20:09:10.477] Loading definitions from package biodb version 1.16.0.
INFO  [20:09:11.172] Enable offline.
INFO  [20:09:11.175] Disable offline.
INFO  [20:09:11.666] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/chebi_extract.tsv".
INFO  [20:09:12.133] Connector "comp.csv.file" deleted.
INFO  [20:09:12.297] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/chebi_extract_custom.csv".
WARN  [20:09:12.300] Column "ID" does not match any biodb field.
WARN  [20:09:12.305] Column "molmass" does not match any biodb field.
WARN  [20:09:12.307] Column "kegg" does not match any biodb field.
INFO  [20:09:12.481] Connector "comp.csv.file" deleted.
INFO  [20:09:12.487] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/chebi_extract_custom.csv".
INFO  [20:09:14.111] Erasing all files in "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi.ex-0c5076ac2a43d16dbce503a44b09f649".
INFO  [20:09:14.276] 12 entries have been processed.
INFO  [20:09:14.759] hello
INFO  [20:09:14.838] Closing BiodbMain instance...
INFO  [20:09:14.841] Connector "comp.csv.file" deleted.
INFO  [20:09:14.842] Connector "chebi.ex" deleted.
--- finished re-building ‘details.Rmd’

--- re-building ‘entries.Rmd’ using rmarkdown
INFO  [20:09:16.678] Loading definitions from package biodb version 1.16.0.
INFO  [20:09:17.028] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/chebi_extract.tsv".
INFO  [20:09:20.116] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/comp.csv.file-78a8b052b8ad91db0d24259871190bf4" for "comp.csv.file-78a8b052b8ad91db0d24259871190bf4".
INFO  [20:09:20.185] Erasing all files in "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/comp.csv.file-78a8b052b8ad91db0d24259871190bf4".
INFO  [20:09:22.719] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/uniprot_extract.tsv".
INFO  [20:09:22.862] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/expasy_enzyme_extract.tsv".
INFO  [20:09:24.049] Creating empty database.
INFO  [20:09:24.451] Write all entries into "/tmp/RtmppkbSYT/biodb_merged_entries_new_db1207f5c22b385.tsv".
INFO  [20:09:25.177] Closing BiodbMain instance...
INFO  [20:09:25.179] Connector "comp.csv.file" deleted.
INFO  [20:09:25.182] Connector "mass.sqlite" deleted.
INFO  [20:09:25.184] Connector "comp.sqlite" deleted.
INFO  [20:09:25.185] Connector "comp.csv.file.1" deleted.
INFO  [20:09:25.186] Connector "comp.csv.file.2" deleted.
INFO  [20:09:25.187] Connector "comp.csv.file.3" deleted.
[WARNING] Citeproc: citation H not found
--- finished re-building ‘entries.Rmd’

--- re-building ‘new_connector.Rmd’ using rmarkdown
INFO  [20:09:27.902] Loading definitions from package biodb version 1.16.0.
INFO  [20:09:28.225] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi.ex-0c5076ac2a43d16dbce503a44b09f649" for "chebi.ex-0c5076ac2a43d16dbce503a44b09f649".
INFO  [20:09:28.562] 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  [20:09:28.712] 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  [20:09:28.845] 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  [20:09:29.376] 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  [20:09:29.830] 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  [20:09:29.962] 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  [20:09:30.541] 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  [20:09:30.997] 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  [20:09:31.172] 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  [20:09:31.529] 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  [20:09:31.943] Loading definitions from package biodb version 1.16.0.
INFO  [20:09:32.715] 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  [20:09:32.892] 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  [20:09:33.032] 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  [20:09:33.621] 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  [20:09:33.998] 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  [20:09:34.134] 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  [20:09:34.766] 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  [20:09:35.031] 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  [20:09:35.174] 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  [20:09:35.925] 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  [20:09:39.228] 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  [20:10:39.727] 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  [20:10:40.115] 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  [20:10:40.250] 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  [20:10:40.386] 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  [20:10:41.023] 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  [20:10:41.408] 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  [20:10:41.551] 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  [20:10:42.170] 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  [20:10:42.516] 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  [20:10:43.312] Connector "chebi.ex" deleted.
INFO  [20:10:43.938] Loading file database "/private/tmp/RtmpFNx2aW/Rinst11b85408e3713/biodb/extdata/chebi_extract_with_unknown_column.tsv".
WARN  [20:10:43.942] Column "elecCharge" does not match any biodb field.
INFO  [20:10:46.195] Connector "chebi.ex" deleted.
INFO  [20:10:46.472] Closing BiodbMain instance...
INFO  [20:10:46.474] Connector "comp.csv.file" deleted.
INFO  [20:10:46.476] 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