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This page was generated on 2025-03-24 12:36 -0400 (Mon, 24 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 870
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Package 29/217HostnameOS / ArchINSTALLBUILDCHECK
BiocFileCache 2.15.1  (landing page)
Lori Shepherd
Snapshot Date: 2025-03-24 12:00 -0400 (Mon, 24 Mar 2025)
git_url: https://git.bioconductor.org/packages/BiocFileCache
git_branch: devel
git_last_commit: 4b81e18
git_last_commit_date: 2025-01-17 12:25:00 -0400 (Fri, 17 Jan 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped


BUILD results for BiocFileCache on teran2

To the developers/maintainers of the BiocFileCache 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: BiocFileCache
Version: 2.15.1
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocFileCache
StartedAt: 2025-03-24 12:16:39 -0400 (Mon, 24 Mar 2025)
EndedAt: 2025-03-24 12:17:15 -0400 (Mon, 24 Mar 2025)
EllapsedTime: 36.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocFileCache
###
##############################################################################
##############################################################################


* checking for file ‘BiocFileCache/DESCRIPTION’ ... OK
* preparing ‘BiocFileCache’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BiocFileCache.Rmd’ using rmarkdown
pandoc: /tmp/RtmpCaJywX/Rbuild2272142528104a/BiocFileCache/vignettes/BiocFileCache.html: hClose: resource exhausted (No space left on device)
Error: processing vignette 'BiocFileCache.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘BiocFileCache.Rmd’

--- re-building ‘BiocFileCache_Troubleshooting.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device

Quitting from BiocFileCache_Troubleshooting.Rmd:54-57 [create]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'conn' in selecting a method for function 'dbDisconnect': object 'info' not found
---
Backtrace:
    ▆
 1. ├─BiocFileCache::BiocFileCache(path, ask = FALSE)
 2. │ └─BiocFileCache:::.sql_create_db(bfc)
 3. │   ├─base::tryCatch(...)
 4. │   └─BiocFileCache:::.sql_disconnect(info)
 5. │     └─DBI::dbDisconnect(info$con)
 6. └─base::.handleSimpleError(`<fn>`, "object 'info' not found", base::quote(.sql_create_db(bfc)))
 7.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BiocFileCache_Troubleshooting.Rmd' failed with diagnostics:
error in evaluating the argument 'conn' in selecting a method for function 'dbDisconnect': object 'info' not found
--- failed re-building ‘BiocFileCache_Troubleshooting.Rmd’

--- re-building ‘BiocFileCache_UseCases.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device

Quitting from BiocFileCache_UseCases.Rmd:191-221 [ensemblremote]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     ▆
  1. ├─BiocFileCache::bfcrpath(bfc, c(url, url2))
  2. └─BiocFileCache::bfcrpath(bfc, c(url, url2))
  3.   ├─BiocFileCache::bfcremove(x, rmdx)
  4.   └─BiocFileCache::bfcremove(x, rmdx)
  5.     └─BiocFileCache:::.sql_remove_resource(x, rids)
  6.       └─BiocFileCache:::.sql_db_execute(bfc, cmd)
  7.         ├─DBI::dbExecute(con, sql, params = param)
  8.         └─DBI::dbExecute(con, sql, params = param)
  9.           ├─DBI::dbSendStatement(conn, statement, ...)
 10.           └─DBI::dbSendStatement(conn, statement, ...)
 11.             ├─DBI::dbSendQuery(conn, statement, ...)
 12.             └─RSQLite::dbSendQuery(conn, statement, ...)
 13.               └─RSQLite (local) .local(conn, statement, ...)
 14.                 ├─methods::new(...)
 15.                 │ ├─methods::initialize(value, ...)
 16.                 │ └─methods::initialize(value, ...)
 17.                 └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following files failed:
  ‘BiocFileCache.Rmd’ ‘BiocFileCache_Troubleshooting.Rmd’
  ‘BiocFileCache_UseCases.Rmd’

Error: Vignette re-building failed.
Execution halted