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This page was generated on 2025-03-27 12:05 -0400 (Thu, 27 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4420
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 191/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocPkgTools 1.24.0  (landing page)
Sean Davis
Snapshot Date: 2025-03-24 13:00 -0400 (Mon, 24 Mar 2025)
git_url: https://git.bioconductor.org/packages/BiocPkgTools
git_branch: RELEASE_3_20
git_last_commit: 2a4b757
git_last_commit_date: 2024-10-29 10:31:21 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for BiocPkgTools on nebbiolo2

To the developers/maintainers of the BiocPkgTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocPkgTools.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: BiocPkgTools
Version: 1.24.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BiocPkgTools
StartedAt: 2025-03-24 16:28:15 -0400 (Mon, 24 Mar 2025)
EndedAt: 2025-03-24 16:36:41 -0400 (Mon, 24 Mar 2025)
EllapsedTime: 506.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BiocPkgTools
###
##############################################################################
##############################################################################


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

Quitting from BiocPkgTools.Rmd:61-64 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! attempt to write a readonly database
---
Backtrace:
     ▆
  1. ├─utils::head(biocBuildReport())
  2. └─BiocPkgTools::biocBuildReport()
  3.   └─BiocPkgTools::biocBuildReportDB(version, pkgType)
  4.     └─base::Map(...)
  5.       └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
  6.         └─BiocPkgTools (local) `<fn>`(url = dots[[1L]][[4L]], tempfolder = dots[[2L]][[4L]])
  7.           └─BiocPkgTools:::.cache_url_file(url)
  8.             ├─BiocFileCache::bfcneedsupdate(bfc, bquery[["rid"]])
  9.             └─BiocFileCache::bfcneedsupdate(bfc, bquery[["rid"]])
 10.               ├─rids %in% .get_rid_filenotfound(x)
 11.               └─BiocFileCache:::.get_rid_filenotfound(x)
 12.                 ├─BiocFileCache::bfcrpath(bfc)
 13.                 └─BiocFileCache::bfcrpath(bfc)
 14.                   └─BiocFileCache (local) update_time_and_path(x, rids)
 15.                     └─BiocFileCache:::.sql_get_rpath(x, i)
 16.                       └─BiocFileCache:::.sql_get_rtype(bfc, rid)
 17.                         └─BiocFileCache:::.sql_get_field(bfc, rid, "rtype")
 18.                           └─BiocFileCache:::.sql_db_get_query(bfc, cmd)
 19.                             ├─DBI::dbGetQuery(con, sql, param)
 20.                             └─DBI::dbGetQuery(con, sql, param)
 21.                               └─DBI (local) .local(conn, statement, ...)
 22.                                 ├─DBI::dbSendQuery(conn, statement, ...)
 23.                                 └─RSQLite::dbSendQuery(conn, statement, ...)
 24.                                   └─RSQLite (local) .local(conn, statement, ...)
 25.                                     ├─methods::new(...)
 26.                                     │ ├─methods::initialize(value, ...)
 27.                                     │ └─methods::initialize(value, ...)
 28.                                     └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BiocPkgTools.Rmd' failed with diagnostics:
attempt to write a readonly database
--- failed re-building ‘BiocPkgTools.Rmd’

SUMMARY: processing the following file failed:
  ‘BiocPkgTools.Rmd’

Error: Vignette re-building failed.
Execution halted