Multiple platform build/check report for BioC 3.23 - BUILD results for stPipe on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4961
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4690
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4627
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 stPipe on kunpeng2

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

Version: 1.1.2

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

StartedAt: 2026-04-17 02:05:59 -0000 (Fri, 17 Apr 2026)

EndedAt: 2026-04-17 02:12:06 -0000 (Fri, 17 Apr 2026)

EllapsedTime: 366.3 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 stPipe
###
##############################################################################
##############################################################################


* checking for file ‘stPipe/DESCRIPTION’ ... OK
* preparing ‘stPipe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stPipe-vignette.Rmd’ using rmarkdown
trying URL 'https://zenodo.org/records/14920583/files/stPipe_demo_R1.fq.gz?download=1'
Content type 'application/octet-stream' length 74003930 bytes (70.6 MB)
==================================================
downloaded 70.6 MB

trying URL 'https://zenodo.org/records/14920583/files/stPipe_demo_R2.fq.gz?download=1'
Content type 'application/octet-stream' length 99083930 bytes (94.5 MB)
==================================================
downloaded 94.5 MB


Quitting from stPipe-vignette.Rmd:101-103 [Run_ST]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─stPipe::Run_ST(config = demo_config_path, show.config = FALSE)
  2. │ └─pbmcapply::pbmclapply(...)
  3. │   └─parallel::mclapply(...)
  4. │     └─base::lapply(X = X, FUN = FUN, ...)
  5. │       └─stPipe (local) FUN(X[[i]], ...)
  6. └─base::loadNamespace(x)
  7.   ├─base::namespaceImportFrom(...)
  8.   │ └─base::asNamespace(ns)
  9.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 10.     └─base::namespaceImportClasses(...)
 11.       └─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
 12.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'stPipe-vignette.Rmd' failed with diagnostics:
class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
--- failed re-building ‘stPipe-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted