Rapid builds (Linux only) of a subset of BioC 3.21<BR>Report updated every 6 hours - BUILD results for AnnotationForge on teran2

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"	870
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BUILD results for AnnotationForge on teran2

To the developers/maintainers of the AnnotationForge 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: AnnotationForge

Version: 1.49.1

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

StartedAt: 2025-03-25 12:24:34 -0400 (Tue, 25 Mar 2025)

EndedAt: 2025-03-25 12:26:43 -0400 (Tue, 25 Mar 2025)

EllapsedTime: 129.1 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 AnnotationForge
###
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* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* preparing ‘AnnotationForge’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘makeProbePackage.Rmd’ using rmarkdown

See
  ‘/tmp/RtmpFLgEUB/hgu95av2probe.Rcheck/00check.log’
for details.

Warning: closing unused connection 4 (/tmp/Rtmpel5Ove/Rinst20e8031c86d722/AnnotationForge/extdata/HG-U95Av2_probe_tab.gz)
--- finished re-building ‘makeProbePackage.Rmd’

--- re-building ‘MakingNewAnnotationPackages.Rnw’ using knitr
trying URL 'http://rest.uniprot.org/uniprotkb/search?query=P13368%20OR%20Q6GZX4&format=xml'
downloaded 49 KB

--- finished re-building ‘MakingNewAnnotationPackages.Rnw’

--- re-building ‘MakingNewOrganismPackages.Rmd’ using knitr
--- finished re-building ‘MakingNewOrganismPackages.Rmd’

--- re-building ‘SQLForge.Rnw’ using knitr

Quitting from SQLForge.Rnw:176-193 [SQLForge]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     x
  1. \-AnnotationForge::makeDBPackage(...)
  2.   \-AnnotationForge:::.makeHUMANCHIP_DB(...)
  3.     \-AnnotationForge:::popHUMANCHIPDB(...)
  4.       \-AnnotationForge:::appendPubmed(db, subStrs = subStrs, printSchema = printSchema)
  5.         \-AnnotationForge:::makeMapCounts(...)
  6.           +-DBI::dbExecute(db, sql)
  7.           \-DBI::dbExecute(db, sql)
  8.             +-DBI::dbSendStatement(conn, statement, ...)
  9.             \-DBI::dbSendStatement(conn, statement, ...)
 10.               +-DBI::dbSendQuery(conn, statement, ...)
 11.               \-RSQLite::dbSendQuery(conn, statement, ...)
 12.                 \-RSQLite (local) .local(conn, statement, ...)
 13.                   +-methods::new(...)
 14.                   | +-methods::initialize(value, ...)
 15.                   | \-methods::initialize(value, ...)
 16.                   \-RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SQLForge.Rnw' failed with diagnostics:
database or disk is full
--- failed re-building ‘SQLForge.Rnw’

SUMMARY: processing the following file failed:
  ‘SQLForge.Rnw’

Error: Vignette re-building failed.
Execution halted