Rapid builds (Linux only) of a subset of BioC 3.21<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	871
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BUILD results for CompoundDb on teran2

To the developers/maintainers of the CompoundDb package:
- 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: CompoundDb

Version: 1.11.2

Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data CompoundDb

StartedAt: 2025-04-04 12:23:17 -0400 (Fri, 04 Apr 2025)

EndedAt: 2025-04-04 12:23:46 -0400 (Fri, 04 Apr 2025)

EllapsedTime: 28.7 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data CompoundDb
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* checking for file ‘CompoundDb/DESCRIPTION’ ... OK
* preparing ‘CompoundDb’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CompoundDb-usage.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘CompoundDb-usage.Rmd’

--- re-building ‘create-compounddb.Rmd’ using rmarkdown

Quitting from create-compounddb.Rmd:521-526 [unnamed-chunk-22]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     ▆
  1. ├─CompoundDb::insertSpectra(...)
  2. └─CompoundDb::insertSpectra(...)
  3.   └─CompoundDb (local) .local(object, spectra, ...)
  4.     └─CompoundDb:::.insert_msms_spectra(con, new_sD)
  5.       ├─DBI::dbWriteTable(...)
  6.       └─RSQLite::dbWriteTable(...)
  7.         └─RSQLite (local) .local(conn, name, value, ...)
  8.           ├─DBI::dbCreateTable(...)
  9.           └─DBI::dbCreateTable(...)
 10.             ├─DBI::dbExecute(conn, query)
 11.             └─DBI::dbExecute(conn, query)
 12.               ├─DBI::dbSendStatement(conn, statement, ...)
 13.               └─DBI::dbSendStatement(conn, statement, ...)
 14.                 ├─DBI::dbSendQuery(conn, statement, ...)
 15.                 └─RSQLite::dbSendQuery(conn, statement, ...)
 16.                   └─RSQLite (local) .local(conn, statement, ...)
 17.                     ├─methods::new(...)
 18.                     │ ├─methods::initialize(value, ...)
 19.                     │ └─methods::initialize(value, ...)
 20.                     └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'create-compounddb.Rmd' failed with diagnostics:
database or disk is full
--- failed re-building ‘create-compounddb.Rmd’

SUMMARY: processing the following file failed:
  ‘create-compounddb.Rmd’

Error: Vignette re-building failed.
Execution halted