Back to Build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1955/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scRepertoire 2.5.8  (landing page)
Nick Borcherding
Snapshot Date: 2025-10-26 13:45 -0400 (Sun, 26 Oct 2025)
git_url: https://git.bioconductor.org/packages/scRepertoire
git_branch: devel
git_last_commit: 74605e1
git_last_commit_date: 2025-10-17 11:17:01 -0400 (Fri, 17 Oct 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for scRepertoire on kjohnson3

To the developers/maintainers of the scRepertoire package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scRepertoire.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: scRepertoire
Version: 2.5.8
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scRepertoire
StartedAt: 2025-10-26 17:56:33 -0400 (Sun, 26 Oct 2025)
EndedAt: 2025-10-26 17:57:59 -0400 (Sun, 26 Oct 2025)
EllapsedTime: 86.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scRepertoire
###
##############################################################################
##############################################################################


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

Quitting from vignette.Rmd:194-197 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://www.borch.dev/uploads/contigs/b_contigs.csv'
---
Backtrace:
    ▆
 1. └─utils::read.csv("https://www.borch.dev/uploads/contigs/b_contigs.csv")
 2.   └─utils::read.table(...)
 3.     └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://www.borch.dev/uploads/contigs/b_contigs.csv'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted