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"	869
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BUILD results for fishpond on teran2

To the developers/maintainers of the fishpond 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: fishpond

Version: 2.13.0

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

StartedAt: 2025-03-23 12:10:18 -0400 (Sun, 23 Mar 2025)

EndedAt: 2025-03-23 12:11:21 -0400 (Sun, 23 Mar 2025)

EllapsedTime: 63.1 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 fishpond
###
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* checking for file ‘fishpond/DESCRIPTION’ ... OK
* preparing ‘fishpond’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘allelic.Rmd’ using rmarkdown

Quitting from allelic.Rmd:135-142 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     ▆
  1. └─fishpond::makeTx2Tss(edb)
  2.   ├─ensembldb::transcripts(x)
  3.   └─ensembldb::transcripts(x)
  4.     └─ensembldb (local) .local(x, ...)
  5.       ├─ensembldb:::getWhat(...)
  6.       └─ensembldb:::getWhat(...)
  7.         └─ensembldb (local) .local(x, ...)
  8.           └─ensembldb:::.getWhat(...)
  9.             ├─DBI::dbGetQuery(dbconn(x), Q)
 10.             └─DBI::dbGetQuery(dbconn(x), Q)
 11.               └─DBI (local) .local(conn, statement, ...)
 12.                 ├─DBI::dbFetch(rs, n = n, ...)
 13.                 └─RSQLite::dbFetch(rs, n = n, ...)
 14.                   └─RSQLite (local) .local(res, n, ...)
 15.                     └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘swish.Rmd’ using rmarkdown
Failed to query server: Connection timed out

 *** caught segfault ***
address 0x7a06612ace40, cause 'memory not mapped'

 *** caught segfault ***
address 0x7a066121bcd0, cause 'memory not mapped'
Segmentation fault (core dumped)