Multiple platform build/check report for BioC 3.20 - BUILD results for Moonlight2R 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 Moonlight2R on nebbiolo2

To the developers/maintainers of the Moonlight2R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Moonlight2R.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: Moonlight2R

Version: 1.4.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Moonlight2R

StartedAt: 2025-03-24 18:13:52 -0400 (Mon, 24 Mar 2025)

EndedAt: 2025-03-24 18:15:11 -0400 (Mon, 24 Mar 2025)

EllapsedTime: 79.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Moonlight2R
###
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* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* preparing ‘Moonlight2R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Moonlight2R.Rmd’ using rmarkdown

Quitting from Moonlight2R.Rmd:598-600 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
     ▆
  1. └─Moonlight2R::getDataGEO(GEOobject = "GSE20347", platform = "GPL571")
  2.   └─GEOquery::getGEO(GEOobject, GSEMatrix = TRUE, AnnotGPL = TRUE)
  3.     └─GEOquery:::getAndParseGSEMatrices(...)
  4.       └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO))
  5.         ├─xml2::read_html(url)
  6.         └─xml2:::read_html.default(url)
  7.           ├─base::suppressWarnings(...)
  8.           │ └─base::withCallingHandlers(...)
  9.           ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
 10.           └─xml2:::read_xml.character(...)
 11.             └─xml2:::read_xml.connection(...)
 12.               ├─base::open(x, "rb")
 13.               └─base::open.connection(x, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Moonlight2R.Rmd’

SUMMARY: processing the following file failed:
  ‘Moonlight2R.Rmd’

Error: Vignette re-building failed.
Execution halted