Multiple platform build/check report for BioC 3.22 - BUILD results for getDEE2 on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4814
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4603
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4547
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4553
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 getDEE2 on taishan

To the developers/maintainers of the getDEE2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/getDEE2.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: getDEE2

Version: 1.19.3

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data getDEE2

StartedAt: 2025-09-19 00:56:22 -0000 (Fri, 19 Sep 2025)

EndedAt: 2025-09-19 01:00:04 -0000 (Fri, 19 Sep 2025)

EllapsedTime: 221.1 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 getDEE2
###
##############################################################################
##############################################################################


* checking for file ‘getDEE2/DESCRIPTION’ ... OK
* preparing ‘getDEE2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘getDEE2.Rmd’ using rmarkdown
trying URL 'http://dee2.io/metadata/celegans_metadata.tsv.cut'
Content type 'text/tab-separated-values' length 2773993 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

trying URL 'http://dee2.io/cgi-bin/request.sh?org=celegans&x=SRR363796&x=SRR363797&x=SRR363798&x=SRR363799'

Quitting from getDEE2.Rmd:118-126 [example1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `getURL()`:
! 'getURL()' failed:
  URL: http://dee2.io/cgi-bin/request.sh?org=celegans&x=SRR363796&x=SRR363797&x=SRR363798&x=SRR363799
  error: cannot open URL 'http://dee2.io/cgi-bin/request.sh?org=celegans&x=SRR363796&x=SRR363797&x=SRR363798&x=SRR363799'
---
Backtrace:
    ▆
 1. └─getDEE2::getDEE2("celegans", SRRvec, metadata = mdat, counts = "GeneCounts")
 2.   └─getDEE2:::getURL(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'getDEE2.Rmd' failed with diagnostics:
'getURL()' failed:
  URL: http://dee2.io/cgi-bin/request.sh?org=celegans&x=SRR363796&x=SRR363797&x=SRR363798&x=SRR363799
  error: cannot open URL 'http://dee2.io/cgi-bin/request.sh?org=celegans&x=SRR363796&x=SRR363797&x=SRR363798&x=SRR363799'
--- failed re-building ‘getDEE2.Rmd’

SUMMARY: processing the following file failed:
  ‘getDEE2.Rmd’

Error: Vignette re-building failed.
Execution halted