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This page was generated on 2026-02-18 11:57 -0500 (Wed, 18 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4890
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 260/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.2.1  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2026-02-16 13:45 -0500 (Mon, 16 Feb 2026)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: RELEASE_3_22
git_last_commit: 68e85a5
git_last_commit_date: 2025-11-08 17:25:11 -0500 (Sat, 08 Nov 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
See other builds for BulkSignalR in R Universe.


BUILD results for BulkSignalR on nebbiolo2

To the developers/maintainers of the BulkSignalR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BulkSignalR.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: BulkSignalR
Version: 1.2.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BulkSignalR
StartedAt: 2026-02-16 16:44:24 -0500 (Mon, 16 Feb 2026)
EndedAt: 2026-02-16 16:47:14 -0500 (Mon, 16 Feb 2026)
EllapsedTime: 169.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BulkSignalR
###
##############################################################################
##############################################################################


* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* preparing ‘BulkSignalR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BulkSignalR-Configure.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "BulkSignalR-Configure", and the latter is "BulkSignalR : </br> Inference of ligand-receptor interactions from bulk data or spatial transcriptomics". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
[WARNING] Could not parse YAML metadata at line 36 column 1: :2:70: Unexpected '
  '
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'BulkSignalR-Configure.knit'
--- finished re-building ‘BulkSignalR-Configure.Rmd’

--- re-building ‘BulkSignalR-Differential.Rmd’ using rmarkdown
[WARNING] Could not parse YAML metadata at line 35 column 1: :2:70: Unexpected '
  '
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'BulkSignalR-Differential.knit'
--- finished re-building ‘BulkSignalR-Differential.Rmd’

--- re-building ‘BulkSignalR-Main.Rmd’ using rmarkdown

Quitting from BulkSignalR-Main.Rmd:617-649 [spatial1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─ExperimentHub (local) Visium_humanDLPFC()
 2.   └─ExperimentHub:::.get_ExperimentHub()
 3.     └─ExperimentHub::ExperimentHub()
 4.       └─AnnotationHub::.Hub(...)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.               └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BulkSignalR-Main.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘BulkSignalR-Main.Rmd’

SUMMARY: processing the following file failed:
  ‘BulkSignalR-Main.Rmd’

Error: Vignette re-building failed.
Execution halted