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This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 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" 4426
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 332/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.32.0  (landing page)
Stian Lågstad
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/chimeraviz
git_branch: RELEASE_3_20
git_last_commit: 6d15cda
git_last_commit_date: 2024-10-29 10:15:57 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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 chimeraviz on taishan

To the developers/maintainers of the chimeraviz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chimeraviz.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: chimeraviz
Version: 1.32.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data chimeraviz
StartedAt: 2025-03-31 22:21:26 -0000 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 22:24:40 -0000 (Mon, 31 Mar 2025)
EllapsedTime: 193.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data chimeraviz
###
##############################################################################
##############################################################################


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

Quitting from chimeraviz-vignette.Rmd:273-302 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/'
---
Backtrace:
     ▆
  1. └─chimeraviz::plot_fusion(...)
  2.   └─chimeraviz::plot_fusion_separate(...)
  3.     ├─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = "UCSC")
  4.     └─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = "UCSC")
  5.       ├─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = value)
  6.       └─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = value)
  7.         └─BiocGenerics::mapply(...)
  8.           ├─BiocGenerics (local) standardGeneric("mapply")
  9.           │ ├─BiocGenerics::eval(mc, env)
 10.           │ └─base::eval(mc, env)
 11.           │   └─base::eval(mc, env)
 12.           └─base::mapply(...)
 13.             └─GenomeInfoDb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]], "UCSC")
 14.               └─GenomeInfoDb:::.map_NCBI_or_RefSeq_seqlevels_to_UCSC(...)
 15.                 └─GenomeInfoDb::getChromInfoFromUCSC(new_genome, map.NCBI = TRUE)
 16.                   └─GenomeInfoDb:::.get_chrom_info_for_registered_UCSC_genome(...)
 17.                     ├─BiocGenerics::do.call(...)
 18.                     ├─base::do.call(...)
 19.                     └─GenomeInfoDb (local) `<fn>`(...)
 20.                       └─GenomeInfoDb::getChromInfoFromNCBI(assembly_accession, assembly.units = AssemblyUnits)
 21.                         └─GenomeInfoDb:::.get_NCBI_chrom_info_from_accession(...)
 22.                           └─GenomeInfoDb::fetch_assembly_report(accession, assembly_name = assembly_name)
 23.                             └─GenomeInfoDb:::.form_assembly_report_url(...)
 24.                               └─GenomeInfoDb::find_NCBI_assembly_ftp_dir(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'chimeraviz-vignette.Rmd' failed with diagnostics:
cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/'
--- failed re-building ‘chimeraviz-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘chimeraviz-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted