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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 45/217HostnameOS / ArchINSTALLBUILDCHECK
BSgenomeForge 1.7.0  (landing page)
Hervé Pagès
Snapshot Date: 2025-03-24 12:00 -0400 (Mon, 24 Mar 2025)
git_url: https://git.bioconductor.org/packages/BSgenomeForge
git_branch: devel
git_last_commit: b850d52
git_last_commit_date: 2024-10-29 11:19:37 -0400 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped

BUILD results for BSgenomeForge on teran2

To the developers/maintainers of the BSgenomeForge 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: BSgenomeForge
Version: 1.7.0
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data BSgenomeForge
StartedAt: 2025-03-24 12:17:27 -0400 (Mon, 24 Mar 2025)
EndedAt: 2025-03-24 12:18:09 -0400 (Mon, 24 Mar 2025)
EllapsedTime: 42.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘BSgenomeForge/DESCRIPTION’ ... OK
* preparing ‘BSgenomeForge’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘QuickBSgenomeForge.Rmd’ using rmarkdown
trying URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/729/545/GCA_009729545.1_ASM972954v1/GCA_009729545.1_ASM972954v1_genomic.fna.gz'
Content type 'application/x-gzip' length 649859 bytes (634 KB)
==================================================
downloaded 634 KB


Quitting from QuickBSgenomeForge.Rmd:85-90 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.assembly_has_no_assembled_molecules()`:
! This assembly contains no assembled molecules so cannot have circular
  sequences.
---
Backtrace:
    ▆
 1. └─BSgenomeForge::forgeBSgenomeDataPkgFromNCBI(...)
 2.   └─BSgenomeForge:::.extract_NCBI_assembly_info(...)
 3.     └─BSgenomeForge:::get_circ_seqs_for_unregistered_assembly_or_genome(...)
 4.       └─BSgenomeForge:::.assembly_has_no_assembled_molecules(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'QuickBSgenomeForge.Rmd' failed with diagnostics:
This assembly contains no assembled molecules so cannot have circular
  sequences.
--- failed re-building ‘QuickBSgenomeForge.Rmd’

--- re-building ‘AdvancedBSgenomeForge.Rnw’ using Sweave
--- finished re-building ‘AdvancedBSgenomeForge.Rnw’

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

Error: Vignette re-building failed.
Execution halted