Multiple platform build/check report for BioC 3.22 - BUILD results for GRaNIE on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4864
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4652
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4597
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4586
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*

BUILD results for GRaNIE on taishan

To the developers/maintainers of the GRaNIE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.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: GRaNIE

Version: 1.13.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GRaNIE

StartedAt: 2025-10-10 01:09:17 -0000 (Fri, 10 Oct 2025)

EndedAt: 2025-10-10 01:10:51 -0000 (Fri, 10 Oct 2025)

EllapsedTime: 94.0 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 GRaNIE
###
##############################################################################
##############################################################################


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

--- re-building ‘GRaNIE_singleCell_eGRNs.Rmd’ using rmarkdown
--- finished re-building ‘GRaNIE_singleCell_eGRNs.Rmd’

--- re-building ‘GRaNIE_workflow.Rmd’ using rmarkdown

Quitting from GRaNIE_workflow.Rmd:135-156 [importData]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─readr::read_tsv(file_RNA, col_types = cols())
 2. │ └─vroom::vroom(...)
 3. │   └─vroom:::vroom_(...)
 4. ├─base (local) `<fn>`(`<gzcon>`, "rb")
 5. └─base::open.connection(`<gzcon>`, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GRaNIE_workflow.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘GRaNIE_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted