Multiple platform build/check report for BioC 3.20 - BUILD results for methylclock on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4420
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 nebbiolo2

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.

raw results

Summary

Package: methylclock

Version: 1.12.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 methylclock

StartedAt: 2025-03-24 18:05:20 -0400 (Mon, 24 Mar 2025)

EndedAt: 2025-03-24 18:10:15 -0400 (Mon, 24 Mar 2025)

EllapsedTime: 295.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 methylclock
###
##############################################################################
##############################################################################


* 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:530-540 [get_geo_gse19711]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
     ▆
  1. └─GEOquery::getGEO("GSE19711")
  2.   └─GEOquery:::getAndParseGSEMatrices(...)
  3.     └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
  4.       ├─xml2::read_html(url)
  5.       └─xml2:::read_html.default(url)
  6.         ├─base::suppressWarnings(...)
  7.         │ └─base::withCallingHandlers(...)
  8.         ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  9.         └─xml2:::read_xml.character(...)
 10.           └─xml2:::read_xml.connection(...)
 11.             ├─base::open(x, "rb")
 12.             └─base::open.connection(x, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted