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This page was generated on 2026-03-05 15:41 -0500 (Thu, 05 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4894
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 242/435HostnameOS / ArchINSTALLBUILDCHECK
MetaScope 1.10.0  (landing page)
Sean Lu
Snapshot Date: 2026-03-05 08:30 -0500 (Thu, 05 Mar 2026)
git_url: https://git.bioconductor.org/packages/MetaScope
git_branch: RELEASE_3_22
git_last_commit: a4564ba
git_last_commit_date: 2025-10-29 10:05:22 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for MetaScope on nebbiolo2

To the developers/maintainers of the MetaScope 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: MetaScope
Version: 1.10.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MetaScope
StartedAt: 2026-03-05 11:29:49 -0500 (Thu, 05 Mar 2026)
EndedAt: 2026-03-05 11:32:25 -0500 (Thu, 05 Mar 2026)
EllapsedTime: 155.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MetaScope
###
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* checking for file ‘MetaScope/DESCRIPTION’ ... OK
* preparing ‘MetaScope’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MetaScope_vignette.Rmd’ using rmarkdown

Quitting from MetaScope_vignette.Rmd:142-155 [target_lib]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt'
---
Backtrace:
    ▆
 1. └─base::sapply(...)
 2.   └─base::lapply(X = X, FUN = FUN, ...)
 3.     └─MetaScope (local) FUN(X[[i]], ...)
 4.       └─MetaScope:::download_parentkingdom(parent_kingdom, quiet)
 5.         └─MetaScope:::get_table(parent_kingdom)
 6.           └─utils::read.table(...)
 7.             └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MetaScope_vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt'
--- failed re-building ‘MetaScope_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted