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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4822
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4612
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4539
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 methylclock on taishan

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

Version: 1.15.0

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

StartedAt: 2025-08-26 00:57:42 -0000 (Tue, 26 Aug 2025)

EndedAt: 2025-08-26 01:11:30 -0000 (Tue, 26 Aug 2025)

EllapsedTime: 828.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data methylclock
###
##############################################################################
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* checking for file ‘methylclock/DESCRIPTION’ ... OK
* preparing ‘methylclock’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘methylclock.Rmd’ using rmarkdown

Quitting from methylclock.Rmd:209-214 [check]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
     ▆
  1. └─methylclock::checkClocks(TestDataset)
  2.   └─methylclock::load_DNAm_Clocks_data()
  3.     └─methylclockData::get_coefEN()
  4.       └─methylclockData:::get_ExperimentHub()
  5.         └─ExperimentHub::ExperimentHub()
  6.           └─AnnotationHub::.Hub(...)
  7.             └─base::tryCatch(...)
  8.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.                   └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'methylclock.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]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘methylclock.Rmd’

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

Error: Vignette re-building failed.
Execution halted