Multiple platform build/check report for BioC 3.21 - BUILD results for snapcount on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
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 snapcount on kunpeng2

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

Version: 1.19.0

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

StartedAt: 2025-03-26 02:35:23 -0000 (Wed, 26 Mar 2025)

EndedAt: 2025-03-26 02:38:16 -0000 (Wed, 26 Mar 2025)

EllapsedTime: 173.1 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 snapcount
###
##############################################################################
##############################################################################


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

Quitting from snapcount_vignette.Rmd:349-361 [jm]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Transferred a partial file [snaptron.cs.jhu.edu]: transfer closed with outstanding read data remaining
---
Backtrace:
     ▆
  1. ├─snapcount::junction_union(gtex, tcga)
  2. │ └─snapcount:::merge_compilations(..., all = TRUE)
  3. │   └─base::lapply(...)
  4. │     └─snapcount (local) FUN(X[[i]], ...)
  5. │       └─snapcount:::get_compilation_metadata(compilation)
  6. │         └─snapcount:::submit_query(uri)
  7. │           └─httr::GET(uri)
  8. │             └─httr:::request_perform(req, hu$handle$handle)
  9. │               ├─httr:::request_fetch(req$output, req$url, handle)
 10. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 11. │                 └─curl::curl_fetch_memory(url, handle = handle)
 12. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'snapcount_vignette.Rmd' failed with diagnostics:
Transferred a partial file [snaptron.cs.jhu.edu]: transfer closed with outstanding read data remaining
--- failed re-building ‘snapcount_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted